Variant report

Variant	rs28483109
Chromosome Location	chr1:153504759-153504760
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	POLR2A	chr1:153504001-153509011	U87	brain:	n/a	n/a
2	POLR2A	chr1:153504109-153508508	A549	lung:	n/a	n/a
3	RCOR1	chr1:153504717-153505004	K562	blood:	n/a	n/a
4	MAZ	chr1:153504643-153509324	IMR90	lung:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
5	JUND	chr1:153504692-153504881	K562	blood:	n/a	chr1:153504736-153504744
6	POLR2A	chr1:153504494-153509551	HCT-116	colon:	n/a	n/a
7	POLR2A	chr1:153504453-153509352	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:153504553-153505111	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr1:153504672-153509603	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:153504596-153505102	ProgFib	skin:	n/a	n/a
11	POLR2A	chr1:153504009-153509167	U87	brain:	n/a	n/a
12	POLR2A	chr1:153504197-153509314	PBDE	blood:	n/a	n/a
13	CHD1	chr1:153504668-153509572	IMR90	lung:	n/a	n/a
14	SIN3AK20	chr1:153504529-153509673	HCT-116	colon:	n/a	n/a
15	MAFF	chr1:153504619-153504785	K562	blood:	n/a	n/a
16	POLR2A	chr1:153504624-153505107	HCT-116	colon:	n/a	n/a
17	GATA1	chr1:153504497-153505858	PBDE	blood:	n/a	chr1:153504737-153504746
18	POLR2A	chr1:153504050-153509343	PANC-1	pancreas:	n/a	n/a
19	FOS	chr1:153504689-153504877	MCF10A-Er-Src	breast:	n/a	chr1:153504734-153504745 chr1:153504736-153504744
20	POLR2A	chr1:153503811-153509451	U87	brain:	n/a	n/a
21	JUN	chr1:153504594-153506726	K562	blood:	n/a	chr1:153506399-153506406 chr1:153504736-153504744
22	POLR2A	chr1:153504484-153509273	IMR90	lung:	n/a	n/a
23	POLR2A	chr1:153503817-153509136	U87	brain:	n/a	n/a
24	POLR2A	chr1:153504661-153505123	HUVEC	blood vessel:	n/a	n/a
25	FOS	chr1:153504528-153505139	HUVEC	blood vessel:	n/a	chr1:153504734-153504745 chr1:153504736-153504744
26	CTCF	chr1:153504705-153506840	A549	lung:	n/a	chr1:153505773-153505789 chr1:153505476-153505484 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
27	POLR2A	chr1:153504643-153508932	HUVEC	blood vessel:	n/a	n/a
28	POLR2A	chr1:153504382-153509132	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr1:153504438-153509047	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153503911..153505890-chr1:153631477..153634216,2	K562	blood:
2	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:
3	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
4	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
5	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
6	chr1:153504209..153505838-chr1:153511280..153513163,2	K562	blood:
7	chr1:153467541..153469828-chr1:153502709..153505691,2	K562	blood:
8	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
9	chr1:153489101..153490682-chr1:153503610..153505565,2	MCF-7	breast:
10	chr1:153502325..153505921-chr1:153601540..153604182,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238279	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000271853	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000272030	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs16835393	0.92[CEU][hapmap]
rs17695220	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs1810765	1.00[JPT][hapmap]
rs1887039	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap]
rs2094217	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094737	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094738	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248745	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262587	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339696	0.81[AMR][1000 genomes]
rs2480695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480696	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427870	0.93[ASN][1000 genomes]
rs28464843	0.83[AMR][1000 genomes]
rs3762262	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4017737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272569	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs4430277	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap]
rs477339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845351	0.92[CEU][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs4845352	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4845552	0.86[GIH][hapmap]
rs4845554	0.92[CEU][hapmap]
rs532652	0.88[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550597	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs552446	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs585215	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587743	0.92[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs659403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659755	0.81[AMR][1000 genomes]
rs6684970	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs7518306	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs7520093	0.83[AMR][1000 genomes]
rs7534343	0.83[AMR][1000 genomes]
rs7534347	0.83[AMR][1000 genomes]
rs9426945	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427239	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427287	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153489000-153506000	Weak transcription	Gastric	stomach
2	chr1:153495600-153504800	Weak transcription	Spleen	Spleen
3	chr1:153498000-153505800	Weak transcription	Aorta	Aorta
4	chr1:153498200-153505200	Weak transcription	Osteobl	bone
5	chr1:153498200-153506000	Weak transcription	Right Ventricle	heart
6	chr1:153498400-153504800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr1:153498400-153505400	Weak transcription	HSMMtube	muscle
8	chr1:153498800-153505200	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:153498800-153505200	Weak transcription	Right Atrium	heart
10	chr1:153499600-153504800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:153499600-153504800	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:153499600-153505000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:153499600-153505200	Weak transcription	Left Ventricle	heart
14	chr1:153499600-153505200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:153499600-153505400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:153500000-153504800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr1:153500000-153504800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:153500000-153504800	Weak transcription	Placenta	Placenta
19	chr1:153500000-153504800	Weak transcription	NHLF	lung
20	chr1:153500000-153505000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:153500200-153505200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:153500400-153505400	Weak transcription	Fetal Heart	heart
23	chr1:153500600-153504800	Weak transcription	HMEC	breast
24	chr1:153500600-153505200	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:153500800-153504800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:153500800-153504800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:153501800-153505600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:153503000-153504800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:153503000-153504800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:153503000-153505400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:153503200-153505200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:153503400-153504800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:153503400-153505400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:153503400-153507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:153503600-153504800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr1:153503600-153504800	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr1:153503600-153504800	Enhancers	HUVEC	blood vessel
38	chr1:153503600-153505200	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:153503800-153505400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr1:153503800-153507400	Enhancers	Small Intestine	intestine
41	chr1:153504000-153505200	Enhancers	Primary T cells fromperipheralblood	blood
42	chr1:153504000-153505200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr1:153504000-153505200	Enhancers	Dnd41	blood
44	chr1:153504000-153505400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
45	chr1:153504000-153505400	Enhancers	Colonic Mucosa	Colon
46	chr1:153504000-153505400	Enhancers	K562	blood
47	chr1:153504000-153505800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:153504000-153506400	Enhancers	Primary T cells from cord blood	blood
49	chr1:153504000-153507600	Enhancers	Fetal Thymus	thymus
50	chr1:153504200-153504800	Enhancers	Duodenum Mucosa	Duodenum

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