Variant report

Variant	rs6686851
Chromosome Location	chr1:113393059-113393060
allele	C/T
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	POLR2A	chr1:113391987-113393555	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:113391990-113393288	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:113392984-113393302	K562	blood:	n/a	n/a
4	POLR2A	chr1:113392749-113393328	GM12878	blood:	n/a	n/a
5	MYC	chr1:113393014-113393194	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:113392731-113393224	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:113393014-113393171	A549	lung:	n/a	n/a
8	E2F4	chr1:113392947-113393147	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:113392712-113393318	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:113392926-113393159	GM12892	blood:	n/a	n/a
11	POLR2A	chr1:113392843-113393226	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:113392623-113393495	GM12892	blood:	n/a	n/a
13	POLR2A	chr1:113392763-113393361	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:113392832-113393207	GM12878	blood:	n/a	n/a
15	MYC	chr1:113392821-113393368	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr1:113392052-113393544	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr1:113392738-113393230	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:113391944-113393187	HUVEC	blood vessel:	n/a	n/a
19	MYC	chr1:113392090-113393363	MCF10A-Er-Src	breast:	n/a	chr1:113392093-113392104
20	POLR2A	chr1:113391953-113393315	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr1:113392748-113393165	GM12892	blood:	n/a	n/a
22	POLR2A	chr1:113392849-113393245	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:113392122-113393169	HUVEC	blood vessel:	n/a	n/a
24	MYC	chr1:113393020-113393266	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr1:113392809-113393192	Hela-S3	cervix:	n/a	n/a
26	MYC	chr1:113393045-113393192	GM12878	blood:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC16A1-1	chr1:113392302-113393265	XLOC_000966
2	lnc-SLC16A1-1	chr1:113392302-113393265	NONHSAT005284

Variant related genes	Relation type
ENSG00000215866	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11102547	0.84[AFR][1000 genomes]
rs11102551	1.00[AFR][1000 genomes]
rs12057664	0.84[AFR][1000 genomes]
rs12079508	0.84[AFR][1000 genomes]
rs12091736	0.85[AFR][1000 genomes]
rs12091936	0.84[AFR][1000 genomes]
rs12096230	1.00[AFR][1000 genomes]
rs6661753	0.92[AFR][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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113388600-113394600	Weak transcription	Hela-S3	cervix
2	chr1:113391800-113393600	Flanking Active TSS	HUVEC	blood vessel
3	chr1:113391800-113393800	Enhancers	Fetal Brain Male	brain
4	chr1:113391800-113394200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:113391800-113394800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:113392000-113393200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:113392000-113393200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr1:113392000-113393200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:113392000-113393200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
10	chr1:113392000-113393200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
11	chr1:113392000-113393200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
12	chr1:113392000-113393200	Active TSS	HSMM	muscle
13	chr1:113392000-113393200	Active TSS	HSMMtube	muscle
14	chr1:113392000-113393400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:113392000-113393400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:113392000-113393600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:113392000-113394400	Flanking Active TSS	Placenta	Placenta
18	chr1:113392200-113393400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
19	chr1:113392200-113393600	Active TSS	Osteobl	bone
20	chr1:113392400-113393200	Weak transcription	Fetal Heart	heart
21	chr1:113392400-113393200	Active TSS	Right Ventricle	heart
22	chr1:113392400-113393800	Active TSS	Brain Anterior Caudate	brain
23	chr1:113392400-113394800	Active TSS	Duodenum Mucosa	Duodenum
24	chr1:113392400-113397800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:113392600-113393200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:113392600-113393200	Bivalent/Poised TSS	Colonic Mucosa	Colon
27	chr1:113392600-113393600	Active TSS	Brain Cingulate Gyrus	brain
28	chr1:113392600-113394800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:113392800-113393200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
30	chr1:113392800-113393200	Active TSS	Muscle Satellite Cultured Cells	--
31	chr1:113392800-113393200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:113392800-113393200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
33	chr1:113392800-113393200	Bivalent Enhancer	Fetal Lung	lung
34	chr1:113392800-113393200	Active TSS	Placenta Amnion	Placenta Amnion
35	chr1:113392800-113393200	Active TSS	NHLF	lung
36	chr1:113392800-113393400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:113392800-113393600	Active TSS	Fetal Brain Female	brain
38	chr1:113392800-113393800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:113392800-113394400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:113392800-113394600	Weak transcription	HMEC	breast
41	chr1:113392800-113395000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:113392800-113397200	Weak transcription	Pancreas	Pancrea
43	chr1:113393000-113393200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:113393000-113393200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:113393000-113393200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:113393000-113393200	Bivalent Enhancer	Fetal Stomach	stomach
47	chr1:113393000-113393200	Enhancers	NH-A	brain
48	chr1:113393000-113393200	Active TSS	NHEK	skin
49	chr1:113393000-113393600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:113393000-113393800	Enhancers	H1 Cell Line	embryonic stem cell

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