Variant report

Variant	rs6980476
Chromosome Location	chr8:87519315-87519316
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr8:87519202-87521831	GM12891	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:87355027..87357482-chr8:87519258..87521837,2	K562	blood:
2	chr17:56735220..56736743-chr8:87519263..87521949,2	MCF-7	breast:
3	chr8:87518953..87524236-chr8:87524519..87528376,7	K562	blood:
4	chr8:87492324..87497991-chr8:87518822..87522169,6	MCF-7	breast:
5	chr8:87469631..87472468-chr8:87519307..87520867,2	MCF-7	breast:
6	chr8:87498873..87500941-chr8:87519267..87521705,2	K562	blood:
7	chr8:87519046..87522405-chr8:87523698..87528376,9	K562	blood:
8	chr8:86130748..86132685-chr8:87519056..87520763,2	K562	blood:
9	chr8:87488182..87492141-chr8:87519043..87522163,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNGB3-1	chr8:87519224-87519341	NONHSAT127560

No data

Variant related genes	Relation type
RMDN1	TF binding region
ENSG00000123124	Chromatin interaction
ENSG00000254231	Chromatin interaction
ENSG00000085719	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000250569	Chromatin interaction
ENSG00000176623	Chromatin interaction
ENSG00000176731	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10086188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10089169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10089253	0.84[ASN][1000 genomes]
rs10090898	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10090963	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10092168	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs10094332	1.00[ASN][1000 genomes]
rs10095589	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097866	0.84[ASN][1000 genomes]
rs10098365	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100182	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10100247	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10100254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10100368	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10100698	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10106390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10107117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10107571	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10108586	0.84[ASN][1000 genomes]
rs10110096	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10481195	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10956820	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10956822	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10956871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11774253	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11774499	0.82[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11776698	0.84[ASN][1000 genomes]
rs11783382	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11984519	0.90[ASN][1000 genomes]
rs11986423	0.89[GIH][hapmap];1.00[ASN][1000 genomes]
rs11994508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11997927	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11998558	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12155981	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs16915375	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16915389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17681534	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28397606	0.90[ASN][1000 genomes]
rs28416254	0.90[ASN][1000 genomes]
rs28438974	1.00[ASN][1000 genomes]
rs28514445	1.00[ASN][1000 genomes]
rs28540009	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28613262	1.00[ASN][1000 genomes]
rs28687116	1.00[ASN][1000 genomes]
rs2953512	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2953514	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2953515	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2953518	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs2976176	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2976180	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3087641	1.00[CHD][hapmap];0.85[GIH][hapmap];0.90[ASN][1000 genomes]
rs4440616	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs57638937	0.82[ASN][1000 genomes]
rs58837061	0.84[ASN][1000 genomes]
rs6651177	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6651268	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67332431	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6992624	0.90[ASN][1000 genomes]
rs7015772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7018083	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72690416	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72690443	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690445	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690447	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690455	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690457	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72690474	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73688856	0.84[ASN][1000 genomes]
rs73688857	0.88[ASN][1000 genomes]
rs73688858	0.88[ASN][1000 genomes]
rs73688859	0.81[ASN][1000 genomes]
rs73688862	0.88[ASN][1000 genomes]
rs7818436	0.90[ASN][1000 genomes]
rs7823951	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7824873	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7833201	0.97[ASN][1000 genomes]
rs7843399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7844014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9297913	0.90[ASN][1000 genomes]
rs9650128	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9650129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv1023510	chr8:87429001-87874948	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv933966	chr8:87454655-87591558	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6980476	FAM82B	Cis_1M	lymphoblastoid	RTeQTL
rs6980476	FAM82B	cis	cerebellum	SCAN
rs6980476	CPNE3	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87482800-87519600	Weak transcription	HUVEC	blood vessel
2	chr8:87488400-87519800	Weak transcription	Psoas Muscle	Psoas
3	chr8:87494200-87519800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr8:87506600-87520000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr8:87508000-87520200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr8:87508200-87520000	Weak transcription	Stomach Mucosa	stomach
7	chr8:87509400-87519400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr8:87511000-87520200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:87513400-87520000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr8:87514600-87519400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr8:87514600-87520200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr8:87515800-87519400	Strong transcription	Brain Anterior Caudate	brain
13	chr8:87517200-87519800	Weak transcription	Colonic Mucosa	Colon
14	chr8:87517400-87519600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr8:87517400-87519800	Weak transcription	Fetal Brain Male	brain
16	chr8:87517400-87519800	Weak transcription	Spleen	Spleen
17	chr8:87517400-87520000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr8:87517400-87520000	Weak transcription	Brain Angular Gyrus	brain
19	chr8:87517400-87520000	Weak transcription	Fetal Brain Female	brain
20	chr8:87517400-87520400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr8:87517600-87519800	Weak transcription	Small Intestine	intestine
22	chr8:87517600-87520000	Weak transcription	Aorta	Aorta
23	chr8:87517800-87519800	Weak transcription	Colon Smooth Muscle	Colon
24	chr8:87517800-87519800	Weak transcription	HSMMtube	muscle
25	chr8:87517800-87520000	Weak transcription	Brain Germinal Matrix	brain
26	chr8:87517800-87520000	Weak transcription	Right Ventricle	heart
27	chr8:87517800-87520200	Weak transcription	Pancreas	Pancrea
28	chr8:87518000-87519400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr8:87518600-87519400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr8:87518600-87520000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr8:87518800-87519400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:87518800-87519400	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr8:87518800-87519600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr8:87518800-87519600	Enhancers	Fetal Intestine Small	intestine
35	chr8:87518800-87519800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr8:87518800-87520000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:87519000-87519400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr8:87519000-87519400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr8:87519000-87519400	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr8:87519000-87519400	Weak transcription	Primary B cells from cord blood	blood
41	chr8:87519000-87519400	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr8:87519000-87519400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:87519000-87519400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr8:87519000-87519400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr8:87519000-87519400	Weak transcription	Liver	Liver
46	chr8:87519000-87519400	Weak transcription	A549	lung
47	chr8:87519000-87519400	Genic enhancers	Dnd41	blood
48	chr8:87519000-87519400	Weak transcription	Hela-S3	cervix
49	chr8:87519000-87519400	Enhancers	HepG2	liver
50	chr8:87519000-87519400	Transcr. at gene 5' and 3'	K562	blood

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