Variant report

Variant	rs7857220
Chromosome Location	chr9:96025052-96025053
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	EP300	chr9:96024702-96025821	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr9:96024707-96025777	ECC-1	luminal epithelium:	n/a	chr9:96025178-96025185
3	MAX	chr9:96024701-96025180	ECC-1	luminal epithelium:	n/a	n/a
4	ESR1	chr9:96024792-96025091	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr9:96024528-96025834	ECC-1	luminal epithelium:	n/a	chr9:96025178-96025185

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96020313..96022881-chr9:96023232..96025158,2	MCF-7	breast:
2	chr9:96022448..96025366-chr9:96049788..96053547,3	MCF-7	breast:

Variant related genes	Relation type
WNK2	TF binding region
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10992646	1.00[ASN][1000 genomes]
rs10992647	1.00[ASN][1000 genomes]
rs10992649	1.00[ASN][1000 genomes]
rs10992650	1.00[ASN][1000 genomes]
rs10992651	1.00[ASN][1000 genomes]
rs10992654	1.00[ASN][1000 genomes]
rs10992656	1.00[ASN][1000 genomes]
rs10992657	1.00[ASN][1000 genomes]
rs10992661	1.00[ASN][1000 genomes]
rs10992681	0.85[MEX][hapmap];0.92[TSI][hapmap]
rs10992699	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787888	0.85[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11789723	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11793893	0.81[EUR][1000 genomes]
rs12000967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12001073	0.81[EUR][1000 genomes]
rs12002458	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005950	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006039	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552158	1.00[ASN][1000 genomes]
rs13283550	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13287544	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs13289160	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290796	0.92[TSI][hapmap]
rs13296817	0.87[ASW][hapmap];0.88[TSI][hapmap]
rs1931364	1.00[ASN][1000 genomes]
rs34085543	0.81[AMR][1000 genomes]
rs34834050	0.81[AMR][1000 genomes]
rs35199621	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35566702	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081907	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4329328	0.81[EUR][1000 genomes]
rs4744213	1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs55981123	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479471	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479474	0.85[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7022051	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7023262	1.00[ASN][1000 genomes]
rs7032614	1.00[CEU][hapmap]
rs7042943	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848843	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866300	1.00[ASN][1000 genomes]
rs7867954	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7873162	0.92[TSI][hapmap]
rs7874101	0.92[TSI][hapmap]
rs7875384	1.00[MEX][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95995200-96026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:95995600-96030600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr9:96005400-96033800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:96005600-96026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:96008000-96030200	Strong transcription	Fetal Intestine Small	intestine
7	chr9:96008000-96030400	Strong transcription	Fetal Intestine Large	intestine
8	chr9:96008200-96026600	Weak transcription	Spleen	Spleen
9	chr9:96008200-96027600	Weak transcription	Right Atrium	heart
10	chr9:96008800-96026200	Weak transcription	Placenta	Placenta
11	chr9:96011000-96026400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:96011200-96030600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:96011200-96032800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:96011200-96033400	Weak transcription	A549	lung
15	chr9:96011800-96026200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr9:96012800-96032600	Weak transcription	Fetal Brain Male	brain
17	chr9:96013000-96031400	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr9:96014000-96033800	Strong transcription	Stomach Smooth Muscle	stomach
19	chr9:96014400-96025400	Strong transcription	Brain Germinal Matrix	brain
20	chr9:96014400-96032800	Strong transcription	Fetal Brain Female	brain
21	chr9:96014800-96026800	Weak transcription	Fetal Heart	heart
22	chr9:96015400-96026600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr9:96015800-96026200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:96017400-96033200	Weak transcription	Brain Substantia Nigra	brain
25	chr9:96017800-96026400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr9:96017800-96030200	Weak transcription	Brain Angular Gyrus	brain
27	chr9:96018400-96033200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr9:96019200-96026600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr9:96020000-96030000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:96020600-96029200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:96022400-96026400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:96022600-96030800	Enhancers	Fetal Thymus	thymus
33	chr9:96022800-96025400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:96023000-96026000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr9:96023000-96026400	Weak transcription	Brain Anterior Caudate	brain
36	chr9:96023200-96025600	Enhancers	Rectal Mucosa Donor 31	rectum
37	chr9:96023400-96025800	Genic enhancers	Duodenum Mucosa	Duodenum
38	chr9:96023400-96025800	Enhancers	Stomach Mucosa	stomach
39	chr9:96023400-96026400	Weak transcription	Right Ventricle	heart
40	chr9:96023800-96025400	Weak transcription	Colon Smooth Muscle	Colon
41	chr9:96024000-96025400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr9:96024000-96025400	Enhancers	Thymus	Thymus
43	chr9:96024000-96025600	Enhancers	Left Ventricle	heart
44	chr9:96024000-96025600	Enhancers	Psoas Muscle	Psoas
45	chr9:96024000-96025800	Enhancers	Gastric	stomach
46	chr9:96024000-96026800	Genic enhancers	Pancreas	Pancrea
47	chr9:96024200-96025800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr9:96024200-96028200	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr9:96024200-96033600	Strong transcription	Fetal Stomach	stomach
50	chr9:96024400-96026200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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