Variant report

Variant	rs16860643
Chromosome Location	chr2:173371278-173371279
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10207640	1.00[CEU][hapmap]
rs10207654	1.00[CEU][hapmap]
rs10930559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930561	0.82[CHB][hapmap]
rs12052253	1.00[CEU][hapmap]
rs12052385	1.00[CEU][hapmap]
rs12613307	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12615584	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621278	1.00[CEU][hapmap]
rs12622724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap]
rs13414928	1.00[CEU][hapmap]
rs1530864	0.82[CHB][hapmap]
rs1530865	0.82[CHB][hapmap]
rs1574256	1.00[CEU][hapmap]
rs1574259	1.00[CEU][hapmap]
rs16860397	1.00[CEU][hapmap]
rs16860426	1.00[CEU][hapmap]
rs16860438	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16860502	0.95[AFR][1000 genomes]
rs16860513	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs16860515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860576	0.95[AFR][1000 genomes]
rs16860605	0.95[AFR][1000 genomes]
rs16860613	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs16860632	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs16860634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860693	0.82[CHB][hapmap]
rs2293645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293647	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs41383947	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs41482144	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs4405725	1.00[CEU][hapmap]
rs55867175	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56882727	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57244773	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57404607	0.85[EUR][1000 genomes]
rs57587465	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59374567	0.85[EUR][1000 genomes]
rs59476799	0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs59970483	0.85[EUR][1000 genomes]
rs60096331	0.85[EUR][1000 genomes]
rs6730284	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6741759	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6743174	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6748504	0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs6759915	0.95[AFR][1000 genomes]
rs71417403	0.86[AFR][1000 genomes]
rs7591769	0.81[ASN][1000 genomes]
rs7602724	0.86[AFR][1000 genomes]
rs8179584	1.00[YRI][hapmap]
rs9636257	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[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	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

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
2	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr2:173330600-173373200	Strong transcription	NHEK	skin
4	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
8	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:173331000-173373800	Strong transcription	HMEC	breast
11	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:173346400-173371400	Weak transcription	NHLF	lung
13	chr2:173347800-173371600	Weak transcription	Fetal Brain Male	brain
14	chr2:173347800-173376200	Weak transcription	Fetal Heart	heart
15	chr2:173352000-173371400	Weak transcription	Fetal Brain Female	brain
16	chr2:173352000-173374200	Weak transcription	Fetal Lung	lung
17	chr2:173352400-173371400	Weak transcription	Psoas Muscle	Psoas
18	chr2:173356400-173379200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:173356600-173371400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:173356600-173375400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:173356800-173374600	Weak transcription	Fetal Kidney	kidney
22	chr2:173356800-173376000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:173356800-173376200	Weak transcription	Brain Substantia Nigra	brain
24	chr2:173357000-173373000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:173357000-173376000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:173357000-173376000	Weak transcription	Aorta	Aorta
27	chr2:173357200-173376600	Weak transcription	Right Ventricle	heart
28	chr2:173357600-173371400	Weak transcription	NH-A	brain
29	chr2:173357600-173376200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:173358000-173376200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:173359200-173371400	Weak transcription	Lung	lung
32	chr2:173359200-173372400	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:173360400-173371400	Weak transcription	Fetal Muscle Leg	muscle
34	chr2:173360800-173371800	Weak transcription	Thymus	Thymus
35	chr2:173361000-173375600	Weak transcription	Spleen	Spleen
36	chr2:173361200-173373600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:173361200-173375200	Weak transcription	GM12878-XiMat	blood
38	chr2:173361800-173373400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:173362800-173372600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr2:173362800-173372800	Strong transcription	Primary T cells fromperipheralblood	blood
41	chr2:173363600-173372600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:173364600-173372000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr2:173365400-173372600	Weak transcription	Pancreas	Pancrea
44	chr2:173365600-173373000	Weak transcription	Fetal Intestine Small	intestine
45	chr2:173365800-173372200	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:173366200-173374400	Strong transcription	HSMM	muscle
47	chr2:173366800-173371800	Weak transcription	Primary B cells from cord blood	blood
48	chr2:173367400-173376000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:173367600-173374400	Weak transcription	Colonic Mucosa	Colon
50	chr2:173368400-173371600	Strong transcription	Fetal Intestine Large	intestine

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