Variant report

Variant	rs11963780
Chromosome Location	chr6:27663595-27663596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:26054155..26056793-chr6:27661780..27663852,2	MCF-7	breast:
2	chr6:27100391..27103275-chr6:27661781..27664479,3	K562	blood:
3	chr6:27651170..27656145-chr6:27660253..27663653,4	MCF-7	breast:
4	chr6:27661399..27663799-chr6:27664607..27667603,2	MCF-7	breast:
5	chr6:27660759..27663752-chr6:27861076..27863812,2	K562	blood:

Variant related genes	Relation type
ENSG00000196331	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10946941	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11750956	0.81[EUR][1000 genomes]
rs11751859	0.81[EUR][1000 genomes]
rs11753029	0.81[EUR][1000 genomes]
rs11754166	0.81[EUR][1000 genomes]
rs11757320	0.81[EUR][1000 genomes]
rs11757748	0.81[EUR][1000 genomes]
rs11963925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966565	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11970451	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59701161	1.00[ASN][1000 genomes]
rs61025649	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6908615	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73384331	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73385150	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73385153	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73389017	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73389037	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73389064	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7743306	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv883510	chr6:27550712-27730064	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1023673	chr6:27570731-27688782	Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
5	nsv1031337	chr6:27596676-27734884	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv518945	chr6:27634640-27668013	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv437481	chr6:27655096-27683572	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv601204	chr6:27655564-27689502	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv1023808	chr6:27656049-27674354	Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv601205	chr6:27656255-27730064	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27662400-27678000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr6:27662400-27680000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr6:27662400-27680400	Weak transcription	Spleen	Spleen
4	chr6:27662400-27680600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:27662400-27684600	Weak transcription	Lung	lung
6	chr6:27662400-27685600	Weak transcription	Esophagus	oesophagus
7	chr6:27662600-27670000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:27662600-27670800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:27662600-27673200	Weak transcription	Fetal Stomach	stomach
10	chr6:27662600-27678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:27662600-27678600	Weak transcription	Primary B cells from cord blood	blood
12	chr6:27662600-27680600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:27662600-27680800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:27662600-27684000	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr6:27662800-27664200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:27662800-27664800	Enhancers	HepG2	liver
17	chr6:27662800-27668800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:27662800-27668800	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:27662800-27670000	Weak transcription	Primary T cells from cord blood	blood
20	chr6:27662800-27670000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:27662800-27670000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:27662800-27670200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:27662800-27670800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:27662800-27671000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:27662800-27671200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:27662800-27672400	Weak transcription	Fetal Intestine Small	intestine
27	chr6:27662800-27678400	Weak transcription	Fetal Lung	lung
28	chr6:27662800-27678400	Weak transcription	Thymus	Thymus
29	chr6:27662800-27678600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr6:27662800-27684000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr6:27662800-27684800	Weak transcription	Fetal Kidney	kidney
32	chr6:27662800-27688400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:27662800-27688600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:27662800-27689000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr6:27663000-27665200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:27663000-27668800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:27663000-27670000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:27663000-27670800	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr6:27663000-27674600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:27663000-27688600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr6:27663200-27664200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr6:27663200-27664400	Enhancers	Dnd41	blood
43	chr6:27663200-27667000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr6:27663200-27669600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr6:27663200-27670000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr6:27663200-27670000	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:27663200-27670000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:27663200-27670000	Weak transcription	Fetal Intestine Large	intestine
49	chr6:27663200-27670000	Weak transcription	Ovary	ovary
50	chr6:27663200-27670200	Weak transcription	Primary B cells from peripheral blood	blood

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