Variant report

Variant	rs11005262
Chromosome Location	chr10:52101738-52101739
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	POLR2A	chr10:52082643-52104294	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:52100945..52103388-chr10:52103997..52106988,2	MCF-7	breast:

Variant related genes	Relation type
SGMS1	TF binding region
ENSG00000198964	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10508927	1.00[YRI][hapmap]
rs10763382	1.00[YRI][hapmap]
rs10825753	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10825754	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10825882	1.00[YRI][hapmap]
rs10825904	1.00[YRI][hapmap]
rs10825978	1.00[YRI][hapmap]
rs11005212	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005213	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005245	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005278	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11005356	1.00[YRI][hapmap]
rs11005418	1.00[YRI][hapmap]
rs11005614	1.00[YRI][hapmap]
rs11006054	1.00[YRI][hapmap]
rs12217518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1916572	1.00[YRI][hapmap]
rs2233778	0.87[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739989	1.00[YRI][hapmap]
rs61858202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086029	1.00[YRI][hapmap]
rs7096171	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7905772	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs927048	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518071	chr10:51595893-52157935	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1054775	chr10:51595893-52392361	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1053903	chr10:51886486-52163991	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1040661	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1051028	chr10:51886486-52164585	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1037118	chr10:51886486-52167442	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1051087	chr10:51886486-52447295	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv916214	chr10:51886486-52458983	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	nsv918212	chr10:51886486-52465482	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv817412	chr10:51911034-52432990	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	esv2830205	chr10:51978430-52135215	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
12	nsv1053293	chr10:51981959-52102649	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
13	nsv1046850	chr10:52009869-52135542	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
14	nsv540625	chr10:52009869-52135542	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
15	esv2762864	chr10:52030945-52107415	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
16	nsv521273	chr10:52051645-52197847	Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52071000-52102400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr10:52071000-52102600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr10:52071200-52103000	Weak transcription	Fetal Intestine Large	intestine
4	chr10:52071200-52103200	Weak transcription	Thymus	Thymus
5	chr10:52071200-52103400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:52071200-52103400	Weak transcription	Esophagus	oesophagus
7	chr10:52073000-52102800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:52076400-52103200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:52080600-52102600	Weak transcription	Lung	lung
10	chr10:52084000-52103200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:52084400-52103400	Weak transcription	Spleen	Spleen
12	chr10:52085800-52102800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr10:52085800-52103400	Weak transcription	Pancreas	Pancrea
14	chr10:52087000-52102400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr10:52087000-52102600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr10:52087000-52103200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr10:52087000-52103400	Weak transcription	Aorta	Aorta
18	chr10:52087000-52105800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr10:52087000-52106800	Weak transcription	Brain Angular Gyrus	brain
20	chr10:52087200-52102400	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:52087200-52102600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr10:52087200-52102600	Weak transcription	Right Ventricle	heart
23	chr10:52087200-52102600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr10:52087200-52103200	Weak transcription	Fetal Stomach	stomach
25	chr10:52087200-52107400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr10:52087400-52102200	Weak transcription	HUVEC	blood vessel
27	chr10:52087400-52102400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr10:52087400-52102600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr10:52087400-52102800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr10:52087400-52103200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:52087400-52103200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr10:52087400-52103200	Weak transcription	Brain Anterior Caudate	brain
33	chr10:52087400-52104800	Weak transcription	NH-A	brain
34	chr10:52087600-52102400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr10:52087600-52102600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr10:52087600-52106600	Weak transcription	Psoas Muscle	Psoas
37	chr10:52087600-52106600	Weak transcription	Stomach Mucosa	stomach
38	chr10:52087800-52102400	Weak transcription	HMEC	breast
39	chr10:52087800-52102600	Weak transcription	Osteobl	bone
40	chr10:52087800-52102800	Weak transcription	Hela-S3	cervix
41	chr10:52087800-52107400	Weak transcription	NHEK	skin
42	chr10:52088400-52102000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr10:52090600-52102000	Weak transcription	NHLF	lung
44	chr10:52090800-52106800	Weak transcription	NHDF-Ad	bronchial
45	chr10:52092200-52102400	Weak transcription	HepG2	liver
46	chr10:52092200-52103200	Weak transcription	Fetal Intestine Small	intestine
47	chr10:52092200-52103400	Weak transcription	Ovary	ovary
48	chr10:52092200-52104200	Weak transcription	Fetal Heart	heart
49	chr10:52092800-52103000	Genic enhancers	K562	blood
50	chr10:52093200-52102600	Weak transcription	Brain Inferior Temporal Lobe	brain

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