Variant report

Variant	rs11925758
Chromosome Location	chr3:159557538-159557539
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	REST	chr3:159557506-159558056	SK-N-SH	brain:	n/a	chr3:159557699-159557712
2	NRF1	chr3:159557283-159558245	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:159557391-159558491	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr3:159557464-159558183	GM18526	blood:	n/a	n/a
5	TAF7	chr3:159557487-159558188	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr3:159557435-159558249	H1-hESC	embryonic stem cell:	n/a	n/a
7	REST	chr3:159557145-159558748	H1-neurons	neurons:	n/a	chr3:159557699-159557712
8	RAD21	chr3:159557518-159558152	SK-N-SH_RA	brain:	n/a	n/a
9	EP300	chr3:159557445-159557947	SK-N-SH_RA	brain:	n/a	n/a
10	YY1	chr3:159557457-159558178	SK-N-SH_RA	brain:	n/a	n/a
11	POLR2A	chr3:159557382-159558303	H1-neurons	neurons:	n/a	n/a
12	SP4	chr3:159557529-159557906	H1-hESC	embryonic stem cell:	n/a	chr3:159557698-159557709
13	POLR2A	chr3:159557443-159558304	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr3:159557406-159557973	H1-hESC	embryonic stem cell:	n/a	chr3:159557700-159557709 chr3:159557698-159557710 chr3:159557699-159557713 chr3:159557698-159557710 chr3:159557698-159557709
15	RAD21	chr3:159557503-159558107	H1-hESC	embryonic stem cell:	n/a	n/a
16	YY1	chr3:159557406-159558258	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr3:159557455-159558282	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr3:159557430-159558221	H1-neurons	neurons:	n/a	n/a
19	EP300	chr3:159557181-159558868	SK-N-SH	brain:	n/a	chr3:159558265-159558274
20	JUND	chr3:159557528-159557949	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr3:159557446-159558167	H1-hESC	embryonic stem cell:	n/a	n/a
22	GATA2	chr3:159557440-159558194	SH-SY5Y	brain:	n/a	n/a
23	MXI1	chr3:159557251-159560865	SK-N-SH	brain:	n/a	n/a
24	YY1	chr3:159557399-159558295	SK-N-SH	brain:	n/a	n/a
25	EP300	chr3:159557412-159557917	SK-N-SH_RA	brain:	n/a	n/a
26	POLR2A	chr3:159557375-159558050	SK-N-SH	brain:	n/a	n/a
27	TAF1	chr3:159557521-159558234	H1-neurons	neurons:	n/a	n/a
28	CHD2	chr3:159557497-159558037	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr3:159557453-159558241	H1-neurons	neurons:	n/a	n/a
30	REST	chr3:159557487-159558282	H1-neurons	neurons:	n/a	chr3:159557699-159557712
31	CREB1	chr3:159557534-159557854	A549	lung:	n/a	n/a
32	POLR2A	chr3:159557423-159558239	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr3:159557536-159558244	H1-hESC	embryonic stem cell:	n/a	n/a
34	MYC	chr3:159557534-159558223	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr3:159557396-159558320	H1-hESC	embryonic stem cell:	n/a	n/a
36	MAX	chr3:159557443-159558343	SK-N-SH	brain:	n/a	n/a
37	YY1	chr3:159557432-159558300	SK-N-SH_RA	brain:	n/a	n/a
38	MAX	chr3:159557524-159558166	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SCHIP1	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1109156	0.83[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11916871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13064756	0.90[CEU][hapmap]
rs3888010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778776	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56272715	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57440770	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59282676	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59904553	0.81[EUR][1000 genomes]
rs60546885	0.81[EUR][1000 genomes]
rs73168564	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73168573	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73168577	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73168579	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7648556	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9820807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9827940	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9828333	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9831996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846145	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159550200-159557600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:159550200-159557600	Weak transcription	Spleen	Spleen
3	chr3:159551400-159561800	Weak transcription	Aorta	Aorta
4	chr3:159551800-159557600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:159551800-159557600	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:159552800-159557800	Enhancers	HUVEC	blood vessel
7	chr3:159555000-159557800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:159555000-159558000	Weak transcription	A549	lung
9	chr3:159555200-159561600	Weak transcription	NHLF	lung
10	chr3:159555400-159557600	Weak transcription	Placenta	Placenta
11	chr3:159555400-159557800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:159555600-159561800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:159555800-159557600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:159555800-159557600	Weak transcription	Lung	lung
15	chr3:159555800-159557800	Weak transcription	Fetal Heart	heart
16	chr3:159555800-159557800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:159556000-159557600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:159556000-159557600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:159556000-159557600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:159556000-159557600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:159556000-159557600	Weak transcription	Psoas Muscle	Psoas
22	chr3:159556000-159557600	Weak transcription	HSMMtube	muscle
23	chr3:159556000-159558400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:159556000-159558600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:159556000-159558600	Weak transcription	Hela-S3	cervix
26	chr3:159556000-159561800	Weak transcription	NHDF-Ad	bronchial
27	chr3:159556000-159566200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:159556200-159563400	Weak transcription	NHEK	skin
29	chr3:159556400-159557600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:159556600-159557600	Enhancers	Colon Smooth Muscle	Colon
31	chr3:159557000-159557600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:159557000-159557600	Weak transcription	Small Intestine	intestine
33	chr3:159557000-159557600	Enhancers	Osteobl	bone
34	chr3:159557000-159559200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:159557000-159559800	Active TSS	Brain Anterior Caudate	brain
36	chr3:159557000-159560000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:159557200-159557600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr3:159557200-159557600	Weak transcription	Ovary	ovary
39	chr3:159557200-159557600	Enhancers	NH-A	brain
40	chr3:159557200-159559000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr3:159557200-159559400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:159557200-159559800	Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr3:159557200-159560000	Active TSS	Fetal Brain Female	brain
44	chr3:159557200-159560200	Active TSS	Brain Germinal Matrix	brain
45	chr3:159557200-159560800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:159557400-159557600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:159557400-159557600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr3:159557400-159557600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr3:159557400-159557600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
50	chr3:159557400-159557600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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