Variant report

Variant	rs9295739
Chromosome Location	chr6:27662395-27662396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:26054155..26056793-chr6:27661780..27663852,2	MCF-7	breast:
2	chr6:27658926..27663446-chr6:27685398..27690588,6	K562	blood:
3	chr6:27100391..27103275-chr6:27661781..27664479,3	K562	blood:
4	chr6:27651170..27656145-chr6:27660253..27663653,4	MCF-7	breast:
5	chr6:27590776..27592562-chr6:27661680..27663552,2	MCF-7	breast:
6	chr6:27661399..27663799-chr6:27664607..27667603,2	MCF-7	breast:
7	chr6:27661331..27663089-chr6:27665763..27668347,2	K562	blood:
8	chr6:27659790..27663314-chr6:27665578..27668905,6	K562	blood:
9	chr6:27179126..27181346-chr6:27660529..27662958,2	K562	blood:
10	chr6:27653789..27659338-chr6:27659392..27663401,13	K562	blood:
11	chr6:27660759..27663752-chr6:27861076..27863812,2	K562	blood:
12	chr6:27660759..27663376-chr6:27861041..27863812,2	K562	blood:
13	chr6:27651230..27653525-chr6:27660393..27663354,2	MCF-7	breast:
14	chr6:27661232..27663489-chr6:27678201..27680638,2	K562	blood:
15	chr6:27661478..27663340-chr6:27680780..27682655,2	K562	blood:
16	chr6:27661606..27663243-chr6:27719625..27721150,2	K562	blood:
17	chr6:27659151..27662876-chr6:27687364..27691190,4	K562	blood:
18	chr14:24682276..24682781-chr6:27661990..27662656,2	Hela-S3	cervix:
19	chr6:27661813..27662703-chr6:27719579..27720188,2	MCF-7	breast:
20	chr6:27662005..27662637-chr6:31619681..31620477,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ENSG00000204463	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000204444	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000254692	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1010261	0.82[YRI][hapmap]
rs12111051	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16867858	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs16867899	1.00[EUR][1000 genomes]
rs16867901	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16867911	1.00[TSI][hapmap];0.90[YRI][hapmap]
rs169263	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs200955	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs200959	1.00[TSI][hapmap]
rs200962	1.00[EUR][1000 genomes]
rs200970	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs201005	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs2200870	1.00[EUR][1000 genomes]
rs55768730	1.00[EUR][1000 genomes]
rs55965630	1.00[EUR][1000 genomes]
rs55987929	1.00[EUR][1000 genomes]
rs56221999	1.00[EUR][1000 genomes]
rs56262840	1.00[EUR][1000 genomes]
rs56366090	1.00[EUR][1000 genomes]
rs58359716	1.00[EUR][1000 genomes]
rs58700542	1.00[EUR][1000 genomes]
rs6456800	1.00[EUR][1000 genomes]
rs6904979	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs73739117	1.00[EUR][1000 genomes]
rs73739122	1.00[EUR][1000 genomes]
rs73739150	1.00[EUR][1000 genomes]
rs73739606	1.00[EUR][1000 genomes]
rs73739685	1.00[EUR][1000 genomes]
rs73739750	1.00[EUR][1000 genomes]
rs73740805	1.00[EUR][1000 genomes]
rs73740842	1.00[EUR][1000 genomes]
rs73742455	1.00[EUR][1000 genomes]
rs9461396	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468147	0.90[YRI][hapmap]
rs9468160	1.00[YRI][hapmap]
rs9468183	0.82[YRI][hapmap]
rs9468189	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468190	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468197	0.80[AMR][1000 genomes]
rs9468198	0.80[AMR][1000 genomes]
rs9468202	0.80[AMR][1000 genomes]
rs9468205	0.80[AMR][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9295739	Hs.158943	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27660800-27662400	Active TSS	H1 Cell Line	embryonic stem cell
2	chr6:27660800-27662800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr6:27660800-27663000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr6:27660800-27663200	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr6:27660800-27663400	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:27661000-27662400	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:27661000-27662400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:27661000-27662400	Active TSS	K562	blood
9	chr6:27661000-27662600	Active TSS	A549	lung
10	chr6:27661000-27662800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr6:27661000-27663000	Active TSS	iPS-15b Cell Line	embryonic stem cell
12	chr6:27661000-27663200	Active TSS	H9 Cell Line	embryonic stem cell
13	chr6:27661000-27663200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:27661200-27662400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr6:27661200-27662400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr6:27661200-27662400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
17	chr6:27661200-27662400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:27661200-27662400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr6:27661200-27662400	Active TSS	Fetal Intestine Large	intestine
20	chr6:27661200-27662400	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
21	chr6:27661200-27662400	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
22	chr6:27661200-27662600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr6:27661200-27662600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:27661200-27662600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:27661200-27662800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:27661200-27662800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:27661200-27662800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr6:27661200-27662800	Active TSS	Fetal Intestine Small	intestine
29	chr6:27661200-27663000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:27661200-27663000	Active TSS	HMEC	breast
31	chr6:27661200-27663200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:27661200-27663200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:27661400-27662400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:27661400-27662400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr6:27661400-27662400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:27661400-27662400	Active TSS	Primary T helper naive cells from peripheral blood	blood
37	chr6:27661400-27662400	Active TSS	Esophagus	oesophagus
38	chr6:27661400-27662400	Active TSS	Placenta Amnion	Placenta Amnion
39	chr6:27661400-27662400	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr6:27661400-27662400	Active TSS	NHEK	skin
41	chr6:27661400-27662600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr6:27661400-27662600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:27661400-27662600	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
44	chr6:27661400-27662600	Active TSS	Colonic Mucosa	Colon
45	chr6:27661400-27662600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
46	chr6:27661400-27662600	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr6:27661400-27662600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
48	chr6:27661400-27662800	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr6:27661400-27662800	Active TSS	Brain Anterior Caudate	brain
50	chr6:27661400-27662800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain

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