Variant report

Variant	rs9429493
Chromosome Location	chr1:113392339-113392340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr1:113391825-113392891	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:113392004-113392517	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:113391854-113392710	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr1:113391987-113393555	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:113391990-113393288	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr1:113392037-113392692	NB4	blood:	n/a	chr1:113392093-113392104
7	POLR2A	chr1:113392320-113392500	A549	lung:	n/a	n/a
8	MAX	chr1:113392041-113392652	A549	lung:	n/a	chr1:113392093-113392104
9	BACH1	chr1:113391962-113392548	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr1:113392006-113392743	H1-hESC	embryonic stem cell:	n/a	chr1:113392093-113392104
11	POLR2A	chr1:113392059-113392646	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr1:113392135-113392786	SK-N-SH	brain:	n/a	n/a
13	MYC	chr1:113392033-113392555	HUVEC	blood vessel:	n/a	chr1:113392093-113392104
14	CTCF	chr1:113392300-113392450	HUVEC	blood vessel:	n/a	n/a
15	MAX	chr1:113391993-113392818	A549	lung:	n/a	chr1:113392093-113392104
16	POLR2A	chr1:113391932-113392508	ECC-1	luminal epithelium:	n/a	n/a
17	MAX	chr1:113391866-113392816	ECC-1	luminal epithelium:	n/a	chr1:113392093-113392104
18	MXI1	chr1:113392291-113392491	H1-hESC	embryonic stem cell:	n/a	n/a
19	MAX	chr1:113392183-113392629	NB4	blood:	n/a	n/a
20	POLR2A	chr1:113392202-113392634	A549	lung:	n/a	n/a
21	E2F6	chr1:113392117-113392650	A549	lung:	n/a	n/a
22	TEAD4	chr1:113391975-113392391	H1-hESC	embryonic stem cell:	n/a	chr1:113392104-113392113
23	E2F4	chr1:113392230-113392617	MCF10A-Er-Src	breast:	n/a	n/a
24	NRF1	chr1:113392317-113392585	H1-hESC	embryonic stem cell:	n/a	n/a
25	MAX	chr1:113391913-113392801	ECC-1	luminal epithelium:	n/a	chr1:113392093-113392104
26	POLR2A	chr1:113392052-113393544	MCF10A-Er-Src	breast:	n/a	n/a
27	MAX	chr1:113391917-113392846	H1-hESC	embryonic stem cell:	n/a	chr1:113392093-113392104
28	NRF1	chr1:113392135-113392684	SK-N-SH	brain:	n/a	n/a
29	MAX	chr1:113391927-113392765	H1-hESC	embryonic stem cell:	n/a	chr1:113392093-113392104
30	MYC	chr1:113391815-113392662	H1-hESC	embryonic stem cell:	n/a	chr1:113392093-113392104
31	TBP	chr1:113392028-113392507	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr1:113392039-113392496	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:113391944-113393187	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr1:113392022-113392782	HUVEC	blood vessel:	n/a	n/a
35	ZBTB7A	chr1:113392022-113392723	ECC-1	luminal epithelium:	n/a	n/a
36	MYC	chr1:113391787-113392506	MCF10A-Er-Src	breast:	n/a	chr1:113392093-113392104
37	MYC	chr1:113392090-113393363	MCF10A-Er-Src	breast:	n/a	chr1:113392093-113392104
38	E2F6	chr1:113391912-113392829	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr1:113391953-113393315	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr1:113392133-113392639	SK-N-MC	brain:	n/a	n/a
41	POLR2A	chr1:113392122-113393169	HUVEC	blood vessel:	n/a	n/a
42	USF2	chr1:113391963-113392383	H1-hESC	embryonic stem cell:	n/a	chr1:113392132-113392148
43	MAX	chr1:113392101-113392872	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-1	chr1:113392302-113393265	XLOC_000966
2	lnc-SLC16A1-1	chr1:113392302-113392401	XLOC_000966
3	lnc-SLC16A1-1	chr1:113392302-113392437	XLOC_000966
4	lnc-SLC16A1-1	chr1:113392302-113393265	NONHSAT005284
5	lnc-SLC16A1-1	chr1:113392302-113392399	ENSG00000215866.3

Variant related genes	Relation type
ENSG00000224167	TF binding region

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11102546	0.84[ASN][1000 genomes]
rs11102549	1.00[ASN][1000 genomes]
rs11102550	1.00[ASN][1000 genomes]
rs11102552	1.00[ASN][1000 genomes]
rs11102554	1.00[ASN][1000 genomes]
rs11102555	1.00[ASN][1000 genomes]
rs11102556	1.00[ASN][1000 genomes]
rs11578123	0.84[ASN][1000 genomes]
rs11578535	0.84[ASN][1000 genomes]
rs12066438	0.86[ASN][1000 genomes]
rs12066478	1.00[ASN][1000 genomes]
rs12079364	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12081613	0.92[ASN][1000 genomes]
rs12082068	0.92[ASN][1000 genomes]
rs12082284	0.92[ASN][1000 genomes]
rs12083391	0.92[ASN][1000 genomes]
rs12083699	0.92[ASN][1000 genomes]
rs12084078	0.92[ASN][1000 genomes]
rs12085206	0.92[ASN][1000 genomes]
rs12085380	0.92[ASN][1000 genomes]
rs12086719	0.92[ASN][1000 genomes]
rs12087350	0.92[ASN][1000 genomes]
rs12088632	0.92[ASN][1000 genomes]
rs12090523	1.00[ASN][1000 genomes]
rs12092282	1.00[ASN][1000 genomes]
rs12093508	1.00[ASN][1000 genomes]
rs12094711	1.00[ASN][1000 genomes]
rs12094750	1.00[ASN][1000 genomes]
rs12097209	0.92[ASN][1000 genomes]
rs12097373	0.92[ASN][1000 genomes]
rs12741871	0.92[ASN][1000 genomes]
rs12742016	0.92[ASN][1000 genomes]
rs12754894	1.00[ASN][1000 genomes]
rs12756538	0.92[ASN][1000 genomes]
rs34186834	0.92[ASN][1000 genomes]
rs34517984	0.92[ASN][1000 genomes]
rs34789338	1.00[ASN][1000 genomes]
rs34839402	0.92[ASN][1000 genomes]
rs34889921	0.92[ASN][1000 genomes]
rs34903691	1.00[ASN][1000 genomes]
rs34915129	0.92[ASN][1000 genomes]
rs34986359	0.92[ASN][1000 genomes]
rs35086049	0.92[ASN][1000 genomes]
rs35386139	1.00[ASN][1000 genomes]
rs35603180	0.92[ASN][1000 genomes]
rs35744129	0.86[ASN][1000 genomes]
rs6537759	1.00[ASN][1000 genomes]
rs6537760	1.00[ASN][1000 genomes]
rs6662943	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6667358	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667856	1.00[ASN][1000 genomes]
rs6674386	0.92[ASN][1000 genomes]
rs6677225	0.92[ASN][1000 genomes]
rs6677237	0.92[ASN][1000 genomes]
rs6687010	0.92[ASN][1000 genomes]
rs6687045	1.00[ASN][1000 genomes]
rs6687054	0.92[ASN][1000 genomes]
rs6692406	0.92[ASN][1000 genomes]
rs6698018	0.92[ASN][1000 genomes]
rs6702269	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71513997	0.92[ASN][1000 genomes]
rs71514000	0.92[ASN][1000 genomes]
rs71659377	0.92[ASN][1000 genomes]
rs71659378	1.00[ASN][1000 genomes]
rs7513783	0.92[ASN][1000 genomes]
rs7516867	1.00[ASN][1000 genomes]
rs7517501	1.00[ASN][1000 genomes]
rs7520778	1.00[ASN][1000 genomes]
rs7526841	0.86[ASN][1000 genomes]
rs7527193	1.00[ASN][1000 genomes]
rs7527283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528133	0.92[ASN][1000 genomes]
rs7537461	0.92[ASN][1000 genomes]
rs7539492	0.92[ASN][1000 genomes]
rs7539588	0.92[ASN][1000 genomes]
rs7539948	0.92[ASN][1000 genomes]
rs7541584	0.92[ASN][1000 genomes]
rs7543983	0.92[ASN][1000 genomes]
rs7554350	0.92[ASN][1000 genomes]
rs9429494	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9970307	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv818378	chr1:113263711-113434818	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv1008434	chr1:113288282-113447426	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
11	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
12	nsv872160	chr1:113301657-113409751	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1000352	chr1:113350929-113405903	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
14	nsv1011519	chr1:113351374-113402040	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
15	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
16	esv3374684	chr1:113359959-113414316	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
18	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
19	esv3360645	chr1:113375959-113414652	Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
20	esv3362439	chr1:113376621-113450321	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv522967	chr1:113384015-113400990	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113388600-113394600	Weak transcription	Hela-S3	cervix
2	chr1:113391800-113392600	Active TSS	Brain Germinal Matrix	brain
3	chr1:113391800-113392800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:113391800-113392800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:113391800-113393000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr1:113391800-113393000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:113391800-113393000	Active TSS	A549	lung
8	chr1:113391800-113393600	Flanking Active TSS	HUVEC	blood vessel
9	chr1:113391800-113393800	Enhancers	Fetal Brain Male	brain
10	chr1:113391800-113394200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:113391800-113394800	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr1:113392000-113392400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:113392000-113392400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr1:113392000-113392400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:113392000-113392400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:113392000-113392400	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr1:113392000-113392400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
18	chr1:113392000-113392400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
19	chr1:113392000-113392400	Flanking Active TSS	Brain Substantia Nigra	brain
20	chr1:113392000-113392400	Flanking Active TSS	Fetal Brain Female	brain
21	chr1:113392000-113392400	Enhancers	Fetal Heart	heart
22	chr1:113392000-113392400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
23	chr1:113392000-113392400	Flanking Active TSS	Gastric	stomach
24	chr1:113392000-113392400	Active TSS	Psoas Muscle	Psoas
25	chr1:113392000-113392400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr1:113392000-113392400	Flanking Active TSS	Right Ventricle	heart
27	chr1:113392000-113392400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
28	chr1:113392000-113392600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
29	chr1:113392000-113392600	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:113392000-113392600	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:113392000-113392600	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:113392000-113392600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr1:113392000-113392600	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
34	chr1:113392000-113392600	Flanking Active TSS	NHEK	skin
35	chr1:113392000-113392800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:113392000-113392800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr1:113392000-113392800	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:113392000-113392800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
39	chr1:113392000-113392800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
40	chr1:113392000-113392800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
41	chr1:113392000-113392800	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:113392000-113392800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:113392000-113392800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:113392000-113392800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr1:113392000-113392800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:113392000-113392800	Flanking Active TSS	Liver	Liver
47	chr1:113392000-113392800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
48	chr1:113392000-113392800	Active TSS	Fetal Kidney	kidney
49	chr1:113392000-113392800	Bivalent Enhancer	Lung	lung
50	chr1:113392000-113392800	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum

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