Variant report

Variant	rs4141966
Chromosome Location	chr9:95572545-95572546
allele	G/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	chr9:95572295-95572624	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr9:95572227-95572571	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr9:95571320-95572648	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95431331..95434473-chr9:95569877..95572688,3	MCF-7	breast:

Variant related genes	Relation type
ANKRD19P	TF binding region
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10821001	0.86[EUR][1000 genomes]
rs10821003	0.86[EUR][1000 genomes]
rs10821004	0.88[EUR][1000 genomes]
rs10821005	0.88[EUR][1000 genomes]
rs10821011	0.87[EUR][1000 genomes]
rs10821014	0.88[EUR][1000 genomes]
rs10992390	0.81[CEU][hapmap]
rs10992396	0.85[EUR][1000 genomes]
rs10992407	0.85[EUR][1000 genomes]
rs10992408	0.85[EUR][1000 genomes]
rs10992409	0.85[EUR][1000 genomes]
rs10992412	0.85[EUR][1000 genomes]
rs10992414	0.85[EUR][1000 genomes]
rs10992416	0.85[EUR][1000 genomes]
rs10992417	0.85[EUR][1000 genomes]
rs10992420	0.86[EUR][1000 genomes]
rs10992422	0.88[EUR][1000 genomes]
rs10992423	0.86[EUR][1000 genomes]
rs10992437	0.86[EUR][1000 genomes]
rs10992448	0.88[EUR][1000 genomes]
rs10992453	0.88[EUR][1000 genomes]
rs10992460	0.89[EUR][1000 genomes]
rs10992461	0.89[EUR][1000 genomes]
rs10992474	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10992475	0.96[ASN][1000 genomes]
rs10992476	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11533010	0.88[EUR][1000 genomes]
rs12057034	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12236754	0.88[EUR][1000 genomes]
rs12238691	0.88[EUR][1000 genomes]
rs12684076	0.84[EUR][1000 genomes]
rs12684587	0.86[EUR][1000 genomes]
rs12685358	0.88[EUR][1000 genomes]
rs1323523	0.81[CEU][hapmap]
rs1575460	0.81[CEU][hapmap]
rs16908555	0.88[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16908560	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1853427	0.96[ASN][1000 genomes]
rs1853428	0.83[EUR][1000 genomes]
rs1853429	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1974004	0.83[EUR][1000 genomes]
rs2146848	0.81[CEU][hapmap]
rs2181584	0.88[EUR][1000 genomes]
rs2398780	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3739605	0.88[EUR][1000 genomes]
rs56311406	0.89[EUR][1000 genomes]
rs57737182	0.89[EUR][1000 genomes]
rs58952648	0.88[EUR][1000 genomes]
rs60498616	0.88[EUR][1000 genomes]
rs7031163	0.88[EUR][1000 genomes]
rs72618187	0.93[ASN][1000 genomes]
rs753804	0.88[EUR][1000 genomes]
rs754600	0.81[EUR][1000 genomes]
rs7850075	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7855203	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7856147	0.81[CEU][hapmap]
rs7857502	0.81[CEU][hapmap]
rs7859967	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7860628	0.89[EUR][1000 genomes]
rs7863741	0.90[EUR][1000 genomes]
rs7869603	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv972420	chr9:95566045-95588965	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95569600-95572600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr9:95570000-95572600	Bivalent Enhancer	Stomach Mucosa	stomach
3	chr9:95570600-95572600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr9:95570600-95572600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr9:95571400-95572600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr9:95571400-95572600	Bivalent Enhancer	Fetal Intestine Large	intestine
7	chr9:95571800-95572600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
8	chr9:95571800-95572600	Bivalent Enhancer	Colon Smooth Muscle	Colon
9	chr9:95572000-95572600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
10	chr9:95572000-95572600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
11	chr9:95572200-95572600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
12	chr9:95572200-95572600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
13	chr9:95572200-95572600	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
14	chr9:95572200-95572600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
15	chr9:95572200-95572600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
16	chr9:95572400-95572600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr9:95572400-95572600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:95572400-95572600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr9:95572400-95572600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:95572400-95572600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
21	chr9:95572400-95572600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
22	chr9:95572400-95572600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr9:95572400-95572600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:95572400-95572600	Bivalent Enhancer	Brain Cingulate Gyrus	brain
25	chr9:95572400-95572600	Bivalent Enhancer	Brain Substantia Nigra	brain

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