Variant report

Variant	rs10125255
Chromosome Location	chr9:101554869-101554870
allele	C/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	GATA3	chr9:101554535-101555253	MCF-7	breast:	n/a	chr9:101554906-101554914
2	GATA3	chr9:101554796-101555047	MCF-7	breast:	n/a	chr9:101554906-101554914
3	GATA3	chr9:101554529-101555146	MCF-7	breast:	n/a	chr9:101554906-101554914
4	NR2F2	chr9:101554627-101555257	MCF-7	breast:	n/a	n/a
5	GATA3	chr9:101554815-101555123	MCF-7	breast:	n/a	chr9:101554906-101554914
6	CEBPD	chr9:101554736-101555193	K562	blood:	n/a	n/a
7	GATA3	chr9:101554865-101555113	SH-SY5Y	brain:	n/a	chr9:101554906-101554914

No.	Distal block	Cell Line	Cell type
1	chr9:101552233..101554875-chr9:101569362..101571456,2	K562	blood:
2	chr9:101535383..101538083-chr9:101553407..101556464,3	MCF-7	breast:
3	chr9:101525358..101528141-chr9:101554411..101556510,2	K562	blood:
4	chr9:101554255..101556910-chr9:101568287..101570321,2	K562	blood:
5	chr9:100964784..100967101-chr9:101553869..101555931,2	K562	blood:
6	chr9:101550194..101555244-chr9:101566657..101571786,8	MCF-7	breast:

Variant related genes	Relation type
ANKS6	TF binding region
ENSG00000119514	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10119228	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10739704	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10987230	1.00[CEU][hapmap]
rs10987234	1.00[CEU][hapmap]
rs10987293	1.00[CEU][hapmap]
rs10987843	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1167771	1.00[CEU][hapmap]
rs1555520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1555522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs180038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs180039	0.91[ASN][1000 genomes]
rs182877	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1930130	1.00[CEU][hapmap]
rs2058881	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2295922	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2778916	1.00[CEU][hapmap]
rs2778919	1.00[CEU][hapmap]
rs2779539	1.00[CEU][hapmap]
rs337527	1.00[CEU][hapmap]
rs337564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337565	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337566	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337567	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337568	0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337570	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs337571	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337580	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs337583	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs337585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs337589	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs337590	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs371521	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4133240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4133831	0.87[EUR][1000 genomes]
rs429562	0.87[EUR][1000 genomes]
rs439347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs453409	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4742740	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4742742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743277	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743279	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4743280	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743283	0.82[EUR][1000 genomes]
rs48418	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs507318	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6415847	0.90[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6415849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs692824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7039118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7846846	0.91[ASN][1000 genomes]
rs7861840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7867234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7867317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9409306	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967932	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101508600-101557400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr9:101518800-101557200	Weak transcription	Psoas Muscle	Psoas
3	chr9:101521200-101557600	Weak transcription	Fetal Brain Male	brain
4	chr9:101530400-101557800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:101534000-101557600	Weak transcription	Right Atrium	heart
6	chr9:101535800-101557400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:101536000-101557600	Weak transcription	Primary B cells from cord blood	blood
8	chr9:101536600-101557600	Weak transcription	Brain Germinal Matrix	brain
9	chr9:101537000-101557400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr9:101544200-101557600	Weak transcription	Colonic Mucosa	Colon
11	chr9:101544800-101557600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr9:101545200-101557200	Weak transcription	Liver	Liver
13	chr9:101546200-101557600	Weak transcription	Left Ventricle	heart
14	chr9:101546400-101557200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:101547000-101557000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr9:101550600-101557000	Weak transcription	Dnd41	blood
17	chr9:101551000-101557400	Weak transcription	Fetal Brain Female	brain
18	chr9:101552400-101556800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr9:101552400-101557000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr9:101552400-101557400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr9:101552600-101557000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr9:101552600-101557000	Weak transcription	Esophagus	oesophagus
23	chr9:101552600-101557200	Weak transcription	Right Ventricle	heart
24	chr9:101552600-101557600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:101552600-101557800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:101552800-101555000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:101552800-101555000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr9:101552800-101555400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr9:101552800-101555800	Enhancers	Stomach Mucosa	stomach
30	chr9:101552800-101556600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr9:101552800-101557200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:101552800-101557200	Weak transcription	Spleen	Spleen
33	chr9:101552800-101557600	Weak transcription	Aorta	Aorta
34	chr9:101553000-101555200	Enhancers	Fetal Intestine Large	intestine
35	chr9:101553000-101555400	Enhancers	Fetal Muscle Leg	muscle
36	chr9:101553200-101555000	Genic enhancers	Fetal Intestine Small	intestine
37	chr9:101553200-101555600	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr9:101553200-101557200	Weak transcription	HepG2	liver
39	chr9:101553200-101558000	Weak transcription	Thymus	Thymus
40	chr9:101553400-101555000	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr9:101553400-101555000	Enhancers	HMEC	breast
42	chr9:101553400-101555600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr9:101553600-101556600	Weak transcription	Brain Anterior Caudate	brain
44	chr9:101553600-101557400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr9:101553600-101557600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr9:101553600-101557800	Weak transcription	GM12878-XiMat	blood
47	chr9:101553800-101555000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:101553800-101556600	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:101553800-101557000	Weak transcription	Brain Substantia Nigra	brain
50	chr9:101553800-101557400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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