Variant report

Variant	rs11695660
Chromosome Location	chr2:10709591-10709592
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HPCAL1-2	chr2:10709128-10709759	NONHSAT069120

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10207845	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1023588	1.00[CEU][hapmap]
rs1045596	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1045597	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045598	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045600	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10490187	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs10929675	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11673879	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11679990	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11684569	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695378	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12151506	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12151843	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12464765	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12468357	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992628	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011270	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011439	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011892	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13018664	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028945	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1990614	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs2110779	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2160257	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2287063	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs2357651	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884231	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34077349	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34187525	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35454239	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35488682	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35551831	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35922089	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3732111	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs3732114	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821196	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4640361	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4668688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4668689	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668692	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4669594	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669595	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4669597	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs4669600	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4669601	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs56038505	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56090656	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138710	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667275	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57633878	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58932234	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59399536	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61515414	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432127	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6432129	1.00[CEU][hapmap]
rs6710687	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6713013	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6716907	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6733161	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6735867	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6748865	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6750803	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6752034	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6754178	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6757809	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7571206	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571318	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594513	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7594816	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7595614	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7598463	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7598994	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7607611	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7607627	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv833370	chr2:10625149-10785402	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1009897	chr2:10627248-10751468	Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10689200-10710600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:10692200-10709600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:10694200-10710000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr2:10696000-10710200	Weak transcription	Left Ventricle	heart
5	chr2:10696600-10710000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:10698200-10709800	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:10698600-10736600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:10698800-10710400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:10699000-10709800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:10699400-10711000	Weak transcription	GM12878-XiMat	blood
11	chr2:10699400-10716200	Weak transcription	Fetal Brain Male	brain
12	chr2:10700800-10709800	Weak transcription	Placenta	Placenta
13	chr2:10700800-10710200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:10700800-10710400	Weak transcription	Fetal Brain Female	brain
15	chr2:10701000-10709600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:10701400-10710200	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:10701800-10710000	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:10702000-10710200	Weak transcription	Ovary	ovary
19	chr2:10702000-10710200	Weak transcription	Right Atrium	heart
20	chr2:10702000-10715800	Weak transcription	Hela-S3	cervix
21	chr2:10702000-10717400	Weak transcription	Psoas Muscle	Psoas
22	chr2:10702200-10710400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:10702200-10713800	Weak transcription	K562	blood
24	chr2:10703400-10710200	Weak transcription	Primary hematopoietic stem cells	blood
25	chr2:10704000-10709600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr2:10704800-10709600	Weak transcription	Lung	lung
27	chr2:10705000-10711800	Weak transcription	Osteobl	bone
28	chr2:10705000-10712400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr2:10705200-10709800	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr2:10705200-10711000	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:10705400-10709600	Weak transcription	Adipose Nuclei	Adipose
32	chr2:10705400-10709800	Weak transcription	Pancreas	Pancrea
33	chr2:10705400-10711200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:10705600-10709800	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:10705600-10711200	Weak transcription	Fetal Lung	lung
36	chr2:10705800-10736000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:10706000-10709600	Strong transcription	Fetal Stomach	stomach
38	chr2:10706000-10713800	Weak transcription	HSMMtube	muscle
39	chr2:10706400-10709800	Weak transcription	NHLF	lung
40	chr2:10706400-10710000	Weak transcription	Brain Angular Gyrus	brain
41	chr2:10706400-10710000	Weak transcription	Brain Anterior Caudate	brain
42	chr2:10706400-10710200	Weak transcription	A549	lung
43	chr2:10706400-10710200	Weak transcription	HMEC	breast
44	chr2:10706400-10713800	Weak transcription	Brain Substantia Nigra	brain
45	chr2:10706400-10716000	Weak transcription	Fetal Kidney	kidney
46	chr2:10706400-10716600	Strong transcription	Fetal Intestine Small	intestine
47	chr2:10707000-10709600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr2:10707000-10709600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:10707000-10710400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:10707200-10709600	Weak transcription	Colonic Mucosa	Colon

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