Variant report

Variant	rs6890869
Chromosome Location	chr5:49966306-49966307
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:49965470..49967570-chr5:49976528..49979367,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10035164	1.00[CHB][hapmap]
rs10036060	1.00[CHB][hapmap]
rs10038842	0.86[EUR][1000 genomes]
rs10039639	0.91[CEU][hapmap]
rs10043477	0.86[EUR][1000 genomes]
rs10044566	1.00[CHB][hapmap]
rs10053011	1.00[CHB][hapmap]
rs10054381	1.00[CHB][hapmap]
rs10056836	1.00[CHB][hapmap]
rs10059085	1.00[CHB][hapmap]
rs10070517	0.88[EUR][1000 genomes]
rs10075034	1.00[CHB][hapmap]
rs10085036	1.00[CHB][hapmap]
rs10434558	1.00[CEU][hapmap]
rs10471940	0.86[EUR][1000 genomes]
rs10471956	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10755235	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10940472	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10940497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11739828	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11750241	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11750771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12188262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12188654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12519006	0.82[EUR][1000 genomes]
rs12521579	0.82[EUR][1000 genomes]
rs12654776	0.84[AFR][1000 genomes]
rs13153982	0.89[EUR][1000 genomes]
rs13164951	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13173734	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13359044	0.82[EUR][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs152102	0.82[EUR][1000 genomes]
rs154133	0.82[EUR][1000 genomes]
rs154135	0.83[EUR][1000 genomes]
rs154137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs154138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs154141	0.82[EUR][1000 genomes]
rs157970	1.00[CEU][hapmap]
rs16884018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs169497	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs171555	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17195388	0.82[EUR][1000 genomes]
rs182230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1823262	0.80[EUR][1000 genomes]
rs1839128	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1988613	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2354526	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2548581	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs2548582	0.81[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs2548583	0.83[EUR][1000 genomes]
rs256340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs256341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs2594706	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26062	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs26065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs26066	0.82[EUR][1000 genomes]
rs26068	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs26069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs26071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[EUR][1000 genomes]
rs2697662	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs27244	0.82[EUR][1000 genomes]
rs27245	1.00[CEU][hapmap]
rs27251	1.00[CEU][hapmap]
rs27357	0.81[EUR][1000 genomes]
rs27389	1.00[CHB][hapmap]
rs27465	0.83[EUR][1000 genomes]
rs27466	0.82[CHB][hapmap]
rs27467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs27468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs27469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs27627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs282549	0.82[EUR][1000 genomes]
rs282550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs282551	0.83[EUR][1000 genomes]
rs282552	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs282553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs282557	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs282559	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs282561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs32376	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs32377	0.82[EUR][1000 genomes]
rs32378	0.82[EUR][1000 genomes]
rs32404	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs32425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs3763367	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs39613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4029420	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs42284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4865628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57079776	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs578198	0.92[CEU][hapmap]
rs62366937	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6450301	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6450359	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6869356	0.91[EUR][1000 genomes]
rs6872496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6886872	0.89[EUR][1000 genomes]
rs6890519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7449019	0.88[EUR][1000 genomes]
rs7711839	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7723361	0.83[CEU][hapmap]
rs7734389	0.86[EUR][1000 genomes]
rs895801	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs921210	1.00[CEU][hapmap];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2757995	chr5:49748352-50058182	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	esv2759342	chr5:49748352-50058182	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv16870	chr5:49885849-49989415	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv818352	chr5:49958221-50017724	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers 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	7 gene(s)	inside rSNPs	diseases
12	nsv968172	chr5:49961360-49966431	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv968910	chr5:49961360-49980983	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6890869	PARP8	Cis_1M	lymphoblastoid	RTeQTL
rs6890869	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49964200-49966400	Weak transcription	Psoas Muscle	Psoas
2	chr5:49964200-49968000	Weak transcription	Spleen	Spleen
3	chr5:49964400-49967800	Weak transcription	Stomach Mucosa	stomach
4	chr5:49964400-49968000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:49964400-49970000	Weak transcription	Aorta	Aorta
6	chr5:49964400-49975400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:49964400-49977400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr5:49964400-49982400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr5:49964400-49983400	Weak transcription	Esophagus	oesophagus
10	chr5:49964600-49969000	Weak transcription	Osteobl	bone
11	chr5:49964800-49966800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:49964800-49967000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:49964800-49967000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr5:49964800-49967800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:49964800-49967800	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:49964800-49968000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:49964800-49968200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:49964800-49968200	Weak transcription	Fetal Stomach	stomach
19	chr5:49964800-49968800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr5:49964800-49969200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:49964800-49969200	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:49964800-49970800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr5:49964800-49976200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:49964800-49976600	Weak transcription	NHDF-Ad	bronchial
25	chr5:49964800-49977600	Weak transcription	Brain Anterior Caudate	brain
26	chr5:49964800-49977800	Weak transcription	Fetal Brain Male	brain
27	chr5:49965000-49966800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr5:49965000-49967800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr5:49965000-49970200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr5:49965400-49967800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr5:49965400-49968400	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:49965400-49968400	Weak transcription	Small Intestine	intestine
33	chr5:49965400-49969400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr5:49965600-49967000	Active TSS	GM12878-XiMat	blood
35	chr5:49965600-49967400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr5:49965600-49967800	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:49965600-49967800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr5:49965600-49967800	Weak transcription	Stomach Smooth Muscle	stomach
39	chr5:49965600-49968000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:49965600-49968000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr5:49965600-49968000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr5:49965600-49968000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:49965600-49968000	Weak transcription	Fetal Heart	heart
44	chr5:49965600-49968200	Weak transcription	Fetal Intestine Large	intestine
45	chr5:49965600-49968600	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr5:49965600-49976400	Weak transcription	HMEC	breast
47	chr5:49965800-49966600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr5:49965800-49967000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr5:49965800-49967000	Enhancers	Primary T cells from cord blood	blood
50	chr5:49965800-49967200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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