Variant report

Variant	rs11898890
Chromosome Location	chr2:173474296-173474297
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	chr2:173473529..173474342-chr2:173574927..173575851,2	MCF-7	breast:
2	chr2:173469296..173470862-chr2:173472263..173475019,2	K562	blood:

Extended variants
information (count: 122 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs10048692	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048707	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10048825	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172894	1.00[CHB][hapmap]
rs10176813	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10186869	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197678	0.93[ASN][1000 genomes]
rs10199472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10201129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10202550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10207262	0.80[ASN][1000 genomes]
rs10208151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427189	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427315	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10451559	0.86[CEU][hapmap]
rs1075638	0.82[EUR][1000 genomes]
rs10930562	0.83[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10930565	0.81[EUR][1000 genomes]
rs11887454	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11890159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891127	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11895461	1.00[CHB][hapmap]
rs11896032	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896178	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897165	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897495	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11897582	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898137	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11901110	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901586	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11902810	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11902907	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11904158	0.80[TSI][hapmap]
rs11904366	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693007	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990751	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13007707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13008835	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13009291	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13010205	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13012115	0.90[CEU][hapmap]
rs13021042	0.89[CEU][hapmap]
rs13023751	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024218	0.80[ASN][1000 genomes]
rs13024431	0.80[ASN][1000 genomes]
rs13032610	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032692	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385644	0.93[ASN][1000 genomes]
rs13386103	1.00[ASN][1000 genomes]
rs13388338	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13392808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13394924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13398305	0.90[CEU][hapmap]
rs13401945	0.80[ASN][1000 genomes]
rs13401980	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13405998	0.80[ASN][1000 genomes]
rs13408780	0.80[ASN][1000 genomes]
rs13415156	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13415174	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13417334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425344	0.80[ASN][1000 genomes]
rs1531151	0.80[ASN][1000 genomes]
rs16860696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740327	0.90[CEU][hapmap]
rs1869922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982410	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290564	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599267	0.80[ASN][1000 genomes]
rs2606069	0.80[ASN][1000 genomes]
rs28537209	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087500	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34139806	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34611798	0.80[ASN][1000 genomes]
rs34707897	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34888332	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35086707	0.80[ASN][1000 genomes]
rs35156154	0.80[ASN][1000 genomes]
rs35665064	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35809888	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35880823	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951155	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999155	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36118221	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3613	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3769321	0.83[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs3792259	0.90[CEU][hapmap]
rs3816536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs56953655	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59004833	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59104969	0.93[ASN][1000 genomes]
rs62167832	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62167835	0.81[EUR][1000 genomes]
rs62169270	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62169301	0.80[ASN][1000 genomes]
rs66460331	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710129	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6723872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6738196	0.83[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6752257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752386	0.81[EUR][1000 genomes]
rs70937080	0.93[ASN][1000 genomes]
rs7566884	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7567092	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7596665	0.90[CEU][hapmap]
rs836589	0.80[ASN][1000 genomes]
rs9287957	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv875415	chr2:173444462-173501069	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875416	chr2:173444462-173504674	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv875417	chr2:173460803-173501069	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv875418	chr2:173460803-173504674	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11898890	LOC440925	cis	parietal	SCAN
rs11898890	PDK1	cis	lymphoblastoid	seeQTL
rs11898890	ZAK	cis	cerebellum	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173431400-173480600	Weak transcription	Gastric	stomach
2	chr2:173444400-173480200	Strong transcription	HepG2	liver
3	chr2:173452000-173479800	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:173452800-173478000	Weak transcription	Fetal Brain Male	brain
5	chr2:173452800-173478600	Weak transcription	Spleen	Spleen
6	chr2:173453800-173478600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:173454200-173475200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:173454400-173477800	Weak transcription	Pancreas	Pancrea
9	chr2:173454400-173479800	Weak transcription	Esophagus	oesophagus
10	chr2:173454400-173489000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:173454600-173477800	Weak transcription	NHLF	lung
12	chr2:173454800-173475200	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr2:173454800-173477800	Weak transcription	Colonic Mucosa	Colon
14	chr2:173454800-173488200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr2:173455200-173480200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr2:173455400-173478400	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:173457200-173480000	Strong transcription	Dnd41	blood
18	chr2:173460800-173479000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:173461400-173488800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:173461400-173504200	Weak transcription	NHEK	skin
21	chr2:173462200-173474800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:173462200-173476600	Weak transcription	Fetal Stomach	stomach
23	chr2:173462200-173477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:173462200-173477800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:173462200-173477800	Weak transcription	Placenta	Placenta
26	chr2:173462200-173478600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:173462200-173479600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:173462200-173481200	Weak transcription	Brain Anterior Caudate	brain
29	chr2:173462200-173481400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:173462200-173507400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr2:173462400-173475400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:173462400-173480800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:173462800-173475000	Weak transcription	Right Ventricle	heart
34	chr2:173462800-173475800	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr2:173462800-173477600	Weak transcription	Fetal Intestine Small	intestine
36	chr2:173462800-173477800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:173462800-173478400	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr2:173462800-173479000	Weak transcription	Thymus	Thymus
39	chr2:173462800-173480800	Weak transcription	Fetal Intestine Large	intestine
40	chr2:173462800-173482400	Weak transcription	Hela-S3	cervix
41	chr2:173462800-173488200	Weak transcription	HSMM	muscle
42	chr2:173463400-173489400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:173464200-173479600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:173464400-173476000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:173464800-173480000	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:173465200-173474400	Strong transcription	Primary B cells from cord blood	blood
47	chr2:173465200-173475200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:173465200-173479400	Strong transcription	Primary T cells from cord blood	blood
49	chr2:173465400-173474600	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr2:173465400-173480000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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