Variant report

Variant	rs3088250
Chromosome Location	chr7:149536855-149536856
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:149466134..149470595-chr7:149532425..149537706,5	MCF-7	breast:
2	chr7:149470096..149472502-chr7:149535858..149537957,2	K562	blood:
3	chr7:149536256..149537911-chr7:149545323..149547402,2	K562	blood:
4	chr7:149520950..149523634-chr7:149534004..149537065,3	K562	blood:
5	chr7:149535432..149538355-chr7:150102358..150106003,3	MCF-7	breast:
6	chr7:149516696..149519376-chr7:149534960..149537116,2	MCF-7	breast:
7	chr7:149535857..149538432-chr7:149551451..149554289,3	MCF-7	breast:
8	chr7:149534427..149538606-chr7:149567610..149571411,8	MCF-7	breast:
9	chr7:149417465..149419893-chr7:149536657..149538216,2	K562	blood:
10	chr7:149520043..149524365-chr7:149535249..149538309,4	MCF-7	breast:
11	chr7:149534468..149539239-chr7:149549126..149555518,7	MCF-7	breast:
12	chr7:149536138..149537939-chr7:149539704..149541464,2	MCF-7	breast:
13	chr7:149534869..149537140-chr7:149569608..149571872,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000204934	Chromatin interaction
ENSG00000133619	Chromatin interaction
ENSG00000181444	Chromatin interaction
ENSG00000171130	Chromatin interaction
ENSG00000196456	Chromatin interaction
ENSG00000106479	Chromatin interaction
ENSG00000197558	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1004200	0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs1008335	0.90[ASN][1000 genomes]
rs10233245	0.88[ASN][1000 genomes]
rs10261203	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10261620	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs10265226	0.89[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs12674102	0.86[ASN][1000 genomes]
rs2040906	0.85[YRI][hapmap]
rs2072169	0.82[ASN][1000 genomes]
rs2074688	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs2074696	0.86[ASN][1000 genomes]
rs2074697	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2247301	0.81[ASN][1000 genomes]
rs28623694	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55776327	0.81[ASN][1000 genomes]
rs55866915	0.80[ASN][1000 genomes]
rs6464034	0.87[ASN][1000 genomes]
rs6957009	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs735499	0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs740113	0.88[ASN][1000 genomes]
rs7778489	0.84[ASN][1000 genomes]
rs7782781	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034350	chr7:149264094-149666356	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv539190	chr7:149264094-149666356	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023901	chr7:149364044-149747442	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv539191	chr7:149364044-149747442	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv469576	chr7:149379626-149563233	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1031581	chr7:149386249-149570178	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv539192	chr7:149386249-149570178	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv831184	chr7:149424835-149600093	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
9	esv2758139	chr7:149441590-149956415	Strong transcription Active TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
10	esv2759571	chr7:149441590-149956415	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
11	nsv889408	chr7:149458623-149539138	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv521861	chr7:149458623-149582906	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv889409	chr7:149458623-149585379	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
14	nsv889411	chr7:149465674-149539138	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1029471	chr7:149496177-149810381	Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
16	nsv539193	chr7:149496177-149810381	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
17	nsv1033095	chr7:149508083-149781872	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
18	nsv608987	chr7:149509981-149547703	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149535400-149537000	Active TSS	NHLF	lung
2	chr7:149535800-149537000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr7:149536000-149537000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:149536000-149537000	Flanking Active TSS	Brain Anterior Caudate	brain
5	chr7:149536000-149537000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr7:149536000-149537000	Flanking Active TSS	Dnd41	blood
7	chr7:149536000-149537200	Flanking Active TSS	Primary T cells from cord blood	blood
8	chr7:149536000-149537200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:149536200-149537000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr7:149536200-149537000	Flanking Active TSS	Colon Smooth Muscle	Colon
11	chr7:149536200-149537000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr7:149536200-149537000	Flanking Active TSS	A549	lung
13	chr7:149536200-149537000	Flanking Active TSS	GM12878-XiMat	blood
14	chr7:149536200-149537200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr7:149536400-149537000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:149536400-149537000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:149536400-149537000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:149536400-149537000	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr7:149536400-149537000	Enhancers	Primary B cells from peripheral blood	blood
20	chr7:149536400-149537000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:149536400-149537000	Enhancers	Adipose Nuclei	Adipose
22	chr7:149536400-149537000	Enhancers	Liver	Liver
23	chr7:149536400-149537000	Enhancers	Fetal Intestine Large	intestine
24	chr7:149536400-149537000	Enhancers	Gastric	stomach
25	chr7:149536400-149537000	Enhancers	Left Ventricle	heart
26	chr7:149536400-149537000	Enhancers	Pancreas	Pancrea
27	chr7:149536400-149537000	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr7:149536400-149537200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr7:149536400-149537200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr7:149536400-149537200	Enhancers	Fetal Brain Male	brain
31	chr7:149536400-149538400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr7:149536400-149539600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr7:149536400-149541400	Weak transcription	Lung	lung
34	chr7:149536400-149542600	Weak transcription	Aorta	Aorta
35	chr7:149536400-149543000	Weak transcription	Ovary	ovary
36	chr7:149536400-149543400	Weak transcription	Placenta	Placenta
37	chr7:149536400-149543800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr7:149536400-149544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr7:149536400-149544800	Weak transcription	Spleen	Spleen
40	chr7:149536400-149547000	Weak transcription	Esophagus	oesophagus
41	chr7:149536400-149556400	Weak transcription	Colonic Mucosa	Colon
42	chr7:149536600-149537000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr7:149536600-149537000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
44	chr7:149536600-149537000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr7:149536600-149537000	Enhancers	Primary T cells fromperipheralblood	blood
46	chr7:149536600-149537000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr7:149536600-149537000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr7:149536600-149537000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr7:149536600-149537000	Enhancers	Brain Hippocampus Middle	brain
50	chr7:149536600-149537000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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