Variant report

Variant	rs10953288
Chromosome Location	chr7:98989626-98989627
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	chr7:98989498-98998154	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr7:98989522-98998944	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr7:98986864-98999101	K562	blood:	n/a	n/a
4	POLR2A	chr7:98989481-98998177	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr7:98989622-98998764	K562	blood:	n/a	n/a
6	POLR2A	chr7:98988204-98999255	K562	blood:	n/a	n/a
7	POLR2A	chr7:98989613-98990188	U87	brain:	n/a	n/a
8	MAX	chr7:98989528-98991000	MCF-7	breast:	n/a	chr7:98990276-98990286 chr7:98990744-98990751 chr7:98990832-98990842 chr7:98990716-98990726 chr7:98990525-98990535 chr7:98990746-98990755
9	POLR2A	chr7:98989619-98992269	K562	blood:	n/a	n/a
10	POLR2A	chr7:98989552-98999005	GM12891	blood:	n/a	n/a
11	POLR2A	chr7:98987820-98994059	HepG2	liver:	n/a	n/a
12	POLR2A	chr7:98989453-98992345	PFSK-1	brain:	n/a	n/a
13	POLR2A	chr7:98989526-98992243	K562	blood:	n/a	n/a
14	NR2F2	chr7:98989566-98991074	MCF-7	breast:	n/a	n/a
15	POLR2A	chr7:98989614-98992266	GM12891	blood:	n/a	n/a
16	POLR2A	chr7:98989468-98999129	GM12878	blood:	n/a	n/a
17	POLR2A	chr7:98989582-98989873	HCT-116	colon:	n/a	n/a
18	POLR2A	chr7:98989544-98989630	HUVEC	blood vessel:	n/a	n/a
19	HDAC2	chr7:98989577-98990978	MCF-7	breast:	n/a	chr7:98990006-98990015

No.	Distal block	Cell Line	Cell type
1	chr7:98933693..98936414-chr7:98989048..98991097,2	MCF-7	breast:
2	chr7:98988826..98993566-chr7:99002963..99006762,7	MCF-7	breast:
3	chr7:98970980..98974747-chr7:98986775..98992580,7	MCF-7	breast:
4	chr7:98976910..98979073-chr7:98989172..98991412,2	MCF-7	breast:
5	chr7:98971244..98973231-chr7:98989224..98993180,5	MCF-7	breast:
6	chr7:98966757..98974253-chr7:98988800..98995304,7	K562	blood:
7	chr7:98922130..98924896-chr7:98987117..98989793,2	K562	blood:

Variant related genes	Relation type
ARPC1B	TF binding region
ENSG00000130429	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000106245	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10085772	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10215765	1.00[ASN][1000 genomes]
rs10215854	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs10226310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10229886	1.00[ASN][1000 genomes]
rs10230784	1.00[ASN][1000 genomes]
rs10235235	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs10236240	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261635	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10264505	1.00[ASN][1000 genomes]
rs10268984	1.00[CHB][hapmap];0.92[GIH][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10273424	1.00[ASN][1000 genomes]
rs10275381	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277447	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10279308	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs10808111	1.00[CHB][hapmap]
rs10808112	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs10953289	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11555142	1.00[ASN][1000 genomes]
rs11760993	0.87[EUR][1000 genomes]
rs11761528	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11766423	1.00[ASN][1000 genomes]
rs11971640	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11972017	1.00[CHB][hapmap]
rs11973173	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs11973801	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11974593	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11974885	1.00[CHB][hapmap]
rs11977673	0.83[GIH][hapmap]
rs11978345	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs11978582	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs11980143	1.00[ASN][1000 genomes]
rs11980995	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11980999	1.00[ASN][1000 genomes]
rs11983474	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12533251	1.00[ASN][1000 genomes]
rs12535424	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12536002	1.00[ASN][1000 genomes]
rs12539480	1.00[ASN][1000 genomes]
rs13223272	1.00[ASN][1000 genomes]
rs13226604	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13227522	1.00[ASN][1000 genomes]
rs13243267	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17161687	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs17161761	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2003498	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2003499	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs28419687	1.00[ASN][1000 genomes]
rs28602855	1.00[ASN][1000 genomes]
rs28627543	1.00[ASN][1000 genomes]
rs34111611	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs34257469	0.89[CEU][hapmap];1.00[CHB][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs35183025	1.00[ASN][1000 genomes]
rs35296070	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs35656351	1.00[ASN][1000 genomes]
rs36104094	1.00[ASN][1000 genomes]
rs45618033	1.00[ASN][1000 genomes]
rs4729532	0.80[CEU][hapmap]
rs4765	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55761861	1.00[ASN][1000 genomes]
rs57786744	1.00[ASN][1000 genomes]
rs57980352	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58964157	1.00[ASN][1000 genomes]
rs60127638	1.00[ASN][1000 genomes]
rs60577432	1.00[ASN][1000 genomes]
rs61740607	1.00[ASN][1000 genomes]
rs66478766	1.00[ASN][1000 genomes]
rs66509940	1.00[ASN][1000 genomes]
rs66568021	1.00[ASN][1000 genomes]
rs66674233	1.00[ASN][1000 genomes]
rs67279166	1.00[ASN][1000 genomes]
rs67309224	1.00[ASN][1000 genomes]
rs67546174	1.00[ASN][1000 genomes]
rs67860332	1.00[ASN][1000 genomes]
rs67909852	1.00[ASN][1000 genomes]
rs67934834	1.00[ASN][1000 genomes]
rs6947826	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6947941	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6947974	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6955490	0.80[CEU][hapmap]
rs6955891	1.00[ASN][1000 genomes]
rs6960805	1.00[CHB][hapmap]
rs6960810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6961579	1.00[CHB][hapmap]
rs704798	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73157587	1.00[ASN][1000 genomes]
rs73157588	1.00[ASN][1000 genomes]
rs73157589	1.00[ASN][1000 genomes]
rs73157590	1.00[ASN][1000 genomes]
rs73157596	1.00[ASN][1000 genomes]
rs73157600	1.00[ASN][1000 genomes]
rs73157601	1.00[ASN][1000 genomes]
rs73157602	1.00[ASN][1000 genomes]
rs73159506	1.00[ASN][1000 genomes]
rs73159509	1.00[ASN][1000 genomes]
rs73159522	1.00[ASN][1000 genomes]
rs73163167	1.00[ASN][1000 genomes]
rs73163169	1.00[ASN][1000 genomes]
rs740160	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[ASN][1000 genomes]
rs7778859	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs868391	1.00[ASN][1000 genomes]
rs9632722	1.00[ASN][1000 genomes]
rs9656060	1.00[ASN][1000 genomes]

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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
3	chr7:98978200-98989800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr7:98979400-99001800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr7:98979600-98989800	Weak transcription	Fetal Heart	heart
6	chr7:98979600-98990200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:98979600-98990200	Weak transcription	Right Atrium	heart
8	chr7:98980400-99003800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr7:98980800-98990000	Strong transcription	NHLF	lung
10	chr7:98980800-99000600	Strong transcription	Dnd41	blood
11	chr7:98981000-98993000	Strong transcription	A549	lung
12	chr7:98981200-98989800	Strong transcription	Fetal Intestine Small	intestine
13	chr7:98981200-98989800	Strong transcription	Thymus	Thymus
14	chr7:98981200-98990000	Strong transcription	K562	blood
15	chr7:98981400-98989800	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr7:98981400-98989800	Strong transcription	Fetal Stomach	stomach
17	chr7:98981600-98989800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:98981800-98989800	Weak transcription	Fetal Brain Male	brain
19	chr7:98982400-98989800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr7:98983000-98989800	Strong transcription	Sigmoid Colon	Sigmoid Colon
21	chr7:98983200-98989800	Strong transcription	Fetal Muscle Trunk	muscle
22	chr7:98983200-98989800	Strong transcription	Lung	lung
23	chr7:98983200-98990000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr7:98983200-98990000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr7:98983200-98990000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr7:98983400-98989800	Strong transcription	Primary B cells from cord blood	blood
27	chr7:98983400-98989800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr7:98983400-98989800	Strong transcription	Adipose Nuclei	Adipose
29	chr7:98983600-98989800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr7:98983600-98989800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:98983600-98989800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:98983800-98990600	Strong transcription	Osteobl	bone
33	chr7:98984000-98989800	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr7:98984000-98989800	Strong transcription	HepG2	liver
35	chr7:98984000-98990000	Strong transcription	Primary T cells from cord blood	blood
36	chr7:98984200-98989800	Strong transcription	Left Ventricle	heart
37	chr7:98984200-98990000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr7:98984200-98990000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr7:98984200-98990000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:98984400-98989800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:98984600-98989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr7:98984600-98990000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:98984600-98990000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr7:98984800-98990400	Weak transcription	Fetal Lung	lung
45	chr7:98985000-98989800	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:98985600-99003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:98985800-98989800	Strong transcription	NH-A	brain
48	chr7:98986200-98990000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr7:98986200-98992000	Weak transcription	HSMMtube	muscle
50	chr7:98987000-98989800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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