Variant report

Variant	rs2953516
Chromosome Location	chr8:87332545-87332546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:87327910..87330150-chr8:87330958..87333182,2	MCF-7	breast:
2	chr8:87329069..87335338-chr8:87352769..87359177,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123124	Chromatin interaction
ENSG00000254231	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10093729	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10095498	0.83[EUR][1000 genomes]
rs10097450	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10098356	0.80[EUR][1000 genomes]
rs10112123	0.82[EUR][1000 genomes]
rs1080170	0.82[EUR][1000 genomes]
rs10956786	0.82[EUR][1000 genomes]
rs10956830	0.83[EUR][1000 genomes]
rs12548328	0.80[EUR][1000 genomes]
rs12549332	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12676754	0.85[EUR][1000 genomes]
rs13254675	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13262672	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13280468	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1436628	0.82[EUR][1000 genomes]
rs28378899	0.81[EUR][1000 genomes]
rs28561640	0.83[EUR][1000 genomes]
rs2917557	0.81[EUR][1000 genomes]
rs2953509	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953510	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953511	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2953517	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976177	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2976178	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976179	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2976181	0.97[ASN][1000 genomes]
rs2976201	0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs41469550	0.84[EUR][1000 genomes]
rs4379426	0.84[EUR][1000 genomes]
rs4464946	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4490816	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4587306	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4623392	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4961188	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6471296	0.86[ASN][1000 genomes]
rs6471309	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6471314	0.84[EUR][1000 genomes]
rs6471316	0.84[EUR][1000 genomes]
rs6985427	0.82[EUR][1000 genomes]
rs6992287	0.84[EUR][1000 genomes]
rs6992944	0.84[EUR][1000 genomes]
rs7003059	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7007855	0.83[EUR][1000 genomes]
rs7017716	0.83[EUR][1000 genomes]
rs7465046	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7816275	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7820234	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7822268	0.82[EUR][1000 genomes]
rs7830480	0.84[EUR][1000 genomes]
rs7832493	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7841690	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv891147	chr8:86886950-87333968	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv429926	chr8:87161695-87429872	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1023114	chr8:87167184-87335197	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1033960	chr8:87167790-87334194	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1016050	chr8:87167790-87335197	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1023772	chr8:87177368-87334194	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1031874	chr8:87177368-87335197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1030401	chr8:87177368-87337260	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	esv2761445	chr8:87185470-87335197	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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 miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv519507	chr8:87187195-87333968	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	esv3360246	chr8:87200232-87419244	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
15	nsv611708	chr8:87205885-87333968	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv1017535	chr8:87261702-87367934	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2953516	FAM82B	Cis_1M	lymphoblastoid	RTeQTL
rs2953516	RMDN1	cis	Whole Blood	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87318400-87333200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:87328600-87333800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr8:87328600-87333800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr8:87330800-87334800	Enhancers	Fetal Lung	lung
5	chr8:87331200-87334400	Weak transcription	Esophagus	oesophagus
6	chr8:87331400-87333400	Weak transcription	Psoas Muscle	Psoas
7	chr8:87332200-87332600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr8:87332200-87332600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr8:87332200-87332600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr8:87332200-87332600	Enhancers	Brain Angular Gyrus	brain
11	chr8:87332200-87332600	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr8:87332200-87332600	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr8:87332200-87332600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr8:87332200-87332800	Flanking Active TSS	A549	lung
15	chr8:87332200-87332800	Flanking Active TSS	HepG2	liver
16	chr8:87332200-87333000	Enhancers	HUVEC	blood vessel
17	chr8:87332200-87333200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
18	chr8:87332200-87333200	Enhancers	Brain Hippocampus Middle	brain
19	chr8:87332200-87333600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr8:87332200-87334200	Enhancers	Ovary	ovary
21	chr8:87332200-87334400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr8:87332200-87334800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr8:87332200-87334800	Enhancers	Placenta	Placenta
24	chr8:87332200-87334800	Enhancers	NHEK	skin
25	chr8:87332400-87332600	Enhancers	Liver	Liver
26	chr8:87332400-87332800	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr8:87332400-87332800	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr8:87332400-87332800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr8:87332400-87332800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr8:87332400-87332800	Active TSS	Adipose Nuclei	Adipose
31	chr8:87332400-87332800	Active TSS	Brain Inferior Temporal Lobe	brain
32	chr8:87332400-87332800	Active TSS	Brain Substantia Nigra	brain
33	chr8:87332400-87332800	Active TSS	Right Atrium	heart
34	chr8:87332400-87333400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:87332400-87333400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr8:87332400-87333600	Weak transcription	Colon Smooth Muscle	Colon
37	chr8:87332400-87334400	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr8:87332400-87334600	Weak transcription	Left Ventricle	heart

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