Variant report

Variant	rs4629023
Chromosome Location	chr17:16980791-16980792
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	chr17:16944416..16947050-chr17:16979219..16983384,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNFRSF13B-4	chr17:16980370-16981066	ENSG00000225442.2

Variant related genes	Relation type
ENSG00000133030	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1047799	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs1047805	0.81[ASN][1000 genomes]
rs10852844	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10852846	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11078368	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078371	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11078372	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11078373	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1110505	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11551189	0.85[ASN][1000 genomes]
rs11651460	0.82[MEX][hapmap]
rs11651938	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11652678	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11654887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11657189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11658084	0.82[MEX][hapmap]
rs11870035	0.87[ASN][1000 genomes]
rs11870483	0.96[ASN][1000 genomes]
rs12451343	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12452303	0.96[AMR][1000 genomes]
rs12601422	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs12602124	0.96[AMR][1000 genomes]
rs12602583	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12602592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12602839	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12603417	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567815	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16961412	0.82[MEX][hapmap]
rs17794784	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs2292526	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2292530	0.94[CHB][hapmap];1.00[CHD][hapmap];0.82[ASN][1000 genomes]
rs2349645	0.87[ASN][1000 genomes]
rs2349648	0.96[ASN][1000 genomes]
rs28452405	0.97[ASN][1000 genomes]
rs34001712	0.97[ASN][1000 genomes]
rs35650871	0.94[ASN][1000 genomes]
rs3744125	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744127	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3744131	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs3744132	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3744133	0.82[MEX][hapmap]
rs3744134	0.94[CHB][hapmap];0.97[CHD][hapmap];0.82[ASN][1000 genomes]
rs3744136	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3744137	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs3744138	0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs3744139	0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs3744140	0.82[MEX][hapmap]
rs3826305	0.80[ASN][1000 genomes]
rs4073688	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4073940	1.00[MEX][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes]
rs4074612	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4074819	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4283273	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4321246	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4468683	0.88[ASN][1000 genomes]
rs4589617	0.81[ASN][1000 genomes]
rs4606773	0.82[MEX][hapmap]
rs4641803	0.84[ASN][1000 genomes]
rs4985703	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985704	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4985714	0.82[MEX][hapmap]
rs4985715	0.92[YRI][hapmap];0.96[AMR][1000 genomes]
rs4985716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985721	0.97[ASN][1000 genomes]
rs4985723	0.96[AMR][1000 genomes]
rs4985728	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4985730	0.96[ASN][1000 genomes]
rs4985737	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4985739	0.82[MEX][hapmap]
rs4985741	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs4985742	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4985743	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56133536	0.87[ASN][1000 genomes]
rs57729820	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs58326998	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59394251	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60128647	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61242604	0.91[ASN][1000 genomes]
rs7212275	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7214429	0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs7216677	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7217970	0.82[MEX][hapmap]
rs7218781	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs7223924	0.96[AMR][1000 genomes]
rs73979060	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73979078	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8066111	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8066234	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs8069259	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8071254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8076273	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs8077360	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9892695	0.85[ASN][1000 genomes]
rs9893676	0.85[ASN][1000 genomes]
rs9897510	0.85[ASN][1000 genomes]
rs9906028	0.94[ASN][1000 genomes]
rs9907109	0.96[ASN][1000 genomes]
rs9910857	0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4629023	M-RIP	Cis_1M	lymphoblastoid	RTeQTL
rs4629023	LOC201164	Cis_1M	lymphoblastoid	RTeQTL
rs4629023	M-RIP	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16952600-16996400	Weak transcription	Fetal Brain Male	brain
2	chr17:16954800-16981200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr17:16955400-16981200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr17:16959200-16982200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr17:16959600-16992000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr17:16966200-16980800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr17:16970000-16981000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:16973000-16981000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr17:16973000-16981200	Enhancers	Brain Anterior Caudate	brain
10	chr17:16973200-16985000	Genic enhancers	A549	lung
11	chr17:16973400-16981400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr17:16973600-16997600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr17:16973800-16982200	Strong transcription	Fetal Brain Female	brain
14	chr17:16974000-16995400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:16974200-16981200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr17:16974200-16981800	Genic enhancers	Fetal Intestine Large	intestine
17	chr17:16974200-16985200	Enhancers	Brain Angular Gyrus	brain
18	chr17:16974400-16985200	Genic enhancers	Fetal Intestine Small	intestine
19	chr17:16975800-16984600	Strong transcription	Primary B cells from cord blood	blood
20	chr17:16976000-16981200	Enhancers	Brain Cingulate Gyrus	brain
21	chr17:16976200-16981200	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr17:16976800-16981600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr17:16977200-16991200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr17:16977400-16981200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr17:16977400-16981200	Weak transcription	Aorta	Aorta
26	chr17:16977400-16981200	Enhancers	Brain Hippocampus Middle	brain
27	chr17:16977400-16992400	Strong transcription	Hela-S3	cervix
28	chr17:16978200-16981000	Weak transcription	Stomach Mucosa	stomach
29	chr17:16978200-16982600	Strong transcription	GM12878-XiMat	blood
30	chr17:16978600-16980800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr17:16978600-16980800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr17:16978600-16981000	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr17:16978600-16981800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr17:16978600-16984200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr17:16978600-16984600	Genic enhancers	Gastric	stomach
36	chr17:16978600-16991000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:16978800-16981200	Weak transcription	Colonic Mucosa	Colon
38	chr17:16978800-16981600	Weak transcription	Fetal Kidney	kidney
39	chr17:16978800-16986400	Genic enhancers	Fetal Muscle Leg	muscle
40	chr17:16978800-16996800	Strong transcription	Dnd41	blood
41	chr17:16979000-16982000	Genic enhancers	Brain Inferior Temporal Lobe	brain
42	chr17:16979000-16983800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr17:16979000-16984800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr17:16979000-16988600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr17:16979000-16989000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr17:16979200-16982200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
47	chr17:16979200-16982600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr17:16979200-16982600	Strong transcription	Brain Germinal Matrix	brain
49	chr17:16979200-16984000	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr17:16979200-16991400	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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