Variant report

Variant	rs6874653
Chromosome Location	chr5:179730843-179730844
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179728336..179731115-chr5:179738243..179739763,2	MCF-7	breast:
2	chr5:179717991..179719935-chr5:179730700..179733372,2	K562	blood:
3	chr5:179724635..179726412-chr5:179729293..179731756,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000050748	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1035411	0.96[CEU][hapmap];0.86[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1035412	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10903252	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11738924	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11739624	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11748619	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12173080	0.87[ASN][1000 genomes]
rs1363517	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2080955	0.84[EUR][1000 genomes]
rs2080959	0.81[ASN][1000 genomes]
rs6879260	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729568	1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7706951	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7730585	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs888922	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs888926	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats 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 miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
6	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases
7	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv10787	chr5:179717724-179732388	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1026417	chr5:179721376-180291360	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179720600-179731400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr5:179720600-179739200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:179720600-179742800	Weak transcription	Right Ventricle	heart
4	chr5:179720600-179743200	Weak transcription	Fetal Lung	lung
5	chr5:179720600-179756800	Weak transcription	NHDF-Ad	bronchial
6	chr5:179720600-179758400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:179720800-179743600	Weak transcription	Right Atrium	heart
8	chr5:179720800-179747000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:179721000-179733600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:179721000-179740800	Weak transcription	Esophagus	oesophagus
11	chr5:179721000-179741000	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:179721000-179741200	Weak transcription	Fetal Brain Male	brain
13	chr5:179721000-179743000	Weak transcription	Spleen	Spleen
14	chr5:179721200-179731400	Weak transcription	A549	lung
15	chr5:179721800-179740800	Weak transcription	Gastric	stomach
16	chr5:179723200-179740800	Weak transcription	Pancreas	Pancrea
17	chr5:179723400-179731200	Weak transcription	Brain Germinal Matrix	brain
18	chr5:179723400-179740600	Weak transcription	Fetal Intestine Small	intestine
19	chr5:179725200-179740800	Weak transcription	Hela-S3	cervix
20	chr5:179726800-179734800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:179726800-179735000	Strong transcription	Osteobl	bone
22	chr5:179726800-179750600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr5:179727000-179735000	Strong transcription	Fetal Stomach	stomach
24	chr5:179727000-179755800	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr5:179727200-179734000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:179727200-179734800	Strong transcription	H9 Cell Line	embryonic stem cell
27	chr5:179727200-179734800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:179727200-179757400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr5:179727200-179757400	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr5:179727400-179731800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:179727400-179734400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr5:179727400-179734600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:179727400-179734600	Strong transcription	Ovary	ovary
34	chr5:179727400-179739800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:179727400-179740000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:179727400-179757600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:179727600-179732200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
38	chr5:179727600-179735000	Strong transcription	NH-A	brain
39	chr5:179727600-179757600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:179727800-179731400	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:179727800-179733600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:179727800-179734400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr5:179727800-179734800	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr5:179728000-179731600	Strong transcription	Fetal Muscle Leg	muscle
45	chr5:179728000-179734000	Strong transcription	Brain Anterior Caudate	brain
46	chr5:179728000-179734600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr5:179728000-179734800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr5:179728200-179732000	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr5:179728600-179731000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr5:179728600-179731000	Weak transcription	Brain Substantia Nigra	brain

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