Variant report

Variant	rs11962534
Chromosome Location	chr6:15360066-15360067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15339598..15341681-chr6:15358454..15361224,2	K562	blood:
2	chr6:15359577..15361259-chr6:15363714..15365800,3	K562	blood:
3	chr6:15247232..15250167-chr6:15358270..15361027,2	MCF-7	breast:
4	chr6:15353509..15355472-chr6:15359724..15361480,2	K562	blood:
5	chr6:15211283..15212939-chr6:15357292..15360132,2	K562	blood:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11970569	1.00[AMR][1000 genomes]
rs16876282	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60399182	0.85[AMR][1000 genomes]
rs73363106	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73363107	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1019927	chr6:15351240-15419257	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv538145	chr6:15351240-15419257	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15327800-15375800	Weak transcription	Aorta	Aorta
2	chr6:15341000-15362800	Weak transcription	Fetal Intestine Small	intestine
3	chr6:15341400-15365400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:15341800-15362800	Weak transcription	Gastric	stomach
5	chr6:15341800-15378400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr6:15342800-15364600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr6:15352000-15363200	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:15352000-15364400	Weak transcription	Esophagus	oesophagus
9	chr6:15352000-15370000	Weak transcription	Lung	lung
10	chr6:15352800-15365600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:15353200-15362200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:15353200-15365400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:15353400-15362600	Weak transcription	A549	lung
14	chr6:15353400-15363600	Weak transcription	Thymus	Thymus
15	chr6:15353400-15364400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:15353400-15365400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:15353600-15365400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:15353800-15362600	Weak transcription	Stomach Mucosa	stomach
19	chr6:15353800-15365400	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr6:15354600-15360800	Weak transcription	NHEK	skin
21	chr6:15354600-15364400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:15354600-15365400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:15354800-15361200	Enhancers	Primary B cells from peripheral blood	blood
24	chr6:15355000-15364400	Weak transcription	Brain Angular Gyrus	brain
25	chr6:15355000-15365400	Weak transcription	HMEC	breast
26	chr6:15355200-15363000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:15356000-15360200	Enhancers	Fetal Stomach	stomach
28	chr6:15356000-15360400	Enhancers	Fetal Lung	lung
29	chr6:15356000-15363200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:15356200-15360200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:15356200-15363800	Weak transcription	Spleen	Spleen
32	chr6:15356400-15365600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr6:15356600-15364200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:15356800-15360200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:15356800-15367000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr6:15357200-15360200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:15357400-15360200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:15357600-15360200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:15357600-15360800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr6:15357600-15363200	Weak transcription	Brain Substantia Nigra	brain
41	chr6:15357800-15360400	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr6:15358000-15365800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr6:15358200-15360400	Enhancers	Primary B cells from cord blood	blood
44	chr6:15358200-15360800	Flanking Active TSS	GM12878-XiMat	blood
45	chr6:15358200-15363600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:15358400-15360400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr6:15358400-15360600	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr6:15358400-15363000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr6:15358600-15360200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:15358600-15367400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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