Variant report

Variant	rs11963854
Chromosome Location	chr6:5626894-5626895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5626232..5628158-chr6:5628361..5630741,2	MCF-7	breast:
2	chr6:5618499..5620610-chr6:5626693..5628979,2	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11962925	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11963668	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11963691	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11964213	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11966192	1.00[ASN][1000 genomes]
rs2326631	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs4960113	0.83[LWK][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes]
rs58102543	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60597164	1.00[EUR][1000 genomes]
rs61427934	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6930787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938074	0.83[YRI][hapmap]
rs73360254	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73360255	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743117	1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7760430	1.00[ASN][1000 genomes]
rs876783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876784	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019428	chr6:5216835-5627839	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv538118	chr6:5216835-5627839	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1016905	chr6:5566364-5639167	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1015549	chr6:5593965-5630468	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5577400-5639800	Weak transcription	Fetal Intestine Small	intestine
2	chr6:5581000-5640400	Weak transcription	Gastric	stomach
3	chr6:5610600-5641000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:5612400-5628000	Weak transcription	Fetal Intestine Large	intestine
5	chr6:5612600-5640000	Weak transcription	Fetal Stomach	stomach
6	chr6:5613000-5627200	Weak transcription	Adipose Nuclei	Adipose
7	chr6:5613200-5640400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:5613600-5627000	Weak transcription	Dnd41	blood
9	chr6:5614400-5639000	Weak transcription	Lung	lung
10	chr6:5614600-5628200	Weak transcription	Ovary	ovary
11	chr6:5614600-5636600	Weak transcription	Pancreas	Pancrea
12	chr6:5614600-5640000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:5614600-5640400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr6:5616200-5627000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:5619600-5627200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr6:5619800-5636800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr6:5620000-5627000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:5620000-5640400	Weak transcription	Spleen	Spleen
19	chr6:5621200-5628600	Weak transcription	Aorta	Aorta
20	chr6:5623400-5628000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:5624600-5627400	Weak transcription	Fetal Brain Male	brain
22	chr6:5624800-5627800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr6:5624800-5628400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:5624800-5629000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr6:5625000-5627600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:5625400-5627200	Enhancers	Primary T cells fromperipheralblood	blood
27	chr6:5625400-5628200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr6:5625400-5630800	Weak transcription	Fetal Heart	heart
29	chr6:5625600-5627000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr6:5625600-5627400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr6:5625800-5628600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:5625800-5634600	Weak transcription	Right Atrium	heart
33	chr6:5625800-5636600	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:5626000-5627000	Enhancers	Primary T cells from cord blood	blood
35	chr6:5626000-5627000	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr6:5626000-5627000	Weak transcription	Fetal Brain Female	brain
37	chr6:5626000-5628000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr6:5626200-5627200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr6:5626200-5628000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:5626200-5628600	Weak transcription	Left Ventricle	heart
41	chr6:5626400-5627000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:5626400-5628000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:5626400-5628000	Enhancers	Fetal Thymus	thymus
44	chr6:5626400-5628200	Enhancers	Primary B cells from cord blood	blood
45	chr6:5626400-5628200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr6:5626600-5627000	Enhancers	GM12878-XiMat	blood
47	chr6:5626600-5628000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr6:5626600-5628200	Enhancers	Primary B cells from peripheral blood	blood
49	chr6:5626600-5631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr6:5626600-5632200	Weak transcription	Rectal Mucosa Donor 31	rectum

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