Variant report

Variant	rs16860515
Chromosome Location	chr2:173342416-173342417
allele	C/T
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]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10207640	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10207654	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10930559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10930561	0.82[CHB][hapmap]
rs12052253	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12052385	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12053442	1.00[AFR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12615596	0.82[EUR][1000 genomes]
rs12621278	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12622724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13421350	0.86[JPT][hapmap]
rs1530864	0.82[CHB][hapmap]
rs1530865	0.82[CHB][hapmap]
rs1574256	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1574259	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16860397	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860419	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16860426	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs16860438	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16860513	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860643	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16860693	0.82[CHB][hapmap]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293647	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4405725	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs55867175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59454075	0.85[EUR][1000 genomes]
rs59476799	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59970483	1.00[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6721624	0.84[JPT][hapmap]
rs6726739	0.86[JPT][hapmap]
rs6730284	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6741759	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6743174	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7564416	0.86[JPT][hapmap]
rs9636257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173321400-173356000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:173327200-173353200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:173327400-173345000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:173327800-173370800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:173328800-173353400	Weak transcription	Right Ventricle	heart
6	chr2:173329400-173344400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:173329800-173371200	Weak transcription	Hela-S3	cervix
8	chr2:173330200-173345600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:173330200-173350400	Weak transcription	Primary B cells from cord blood	blood
10	chr2:173330400-173360400	Weak transcription	Small Intestine	intestine
11	chr2:173330600-173344600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr2:173330600-173344800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:173330600-173344800	Weak transcription	Adipose Nuclei	Adipose
14	chr2:173330600-173345000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:173330600-173345000	Weak transcription	NH-A	brain
16	chr2:173330600-173345200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:173330600-173345600	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:173330600-173346400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr2:173330600-173351400	Weak transcription	Psoas Muscle	Psoas
20	chr2:173330600-173351400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr2:173330600-173351600	Weak transcription	Brain Anterior Caudate	brain
22	chr2:173330600-173352400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr2:173330600-173352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr2:173330600-173352600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:173330600-173353200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr2:173330600-173353200	Weak transcription	Aorta	Aorta
27	chr2:173330600-173353400	Weak transcription	Fetal Stomach	stomach
28	chr2:173330600-173371400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:173330600-173372200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:173330600-173373200	Strong transcription	NHEK	skin
31	chr2:173330600-173373400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr2:173330600-173373400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:173330600-173373600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:173330600-173374200	Weak transcription	Stomach Mucosa	stomach
35	chr2:173330800-173345400	Weak transcription	NHLF	lung
36	chr2:173330800-173348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:173331000-173344800	Weak transcription	NHDF-Ad	bronchial
38	chr2:173331000-173346600	Weak transcription	Brain Cingulate Gyrus	brain
39	chr2:173331000-173348400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:173331000-173370000	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr2:173331000-173373200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:173331000-173373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:173331000-173373800	Strong transcription	HMEC	breast
44	chr2:173331200-173372000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr2:173331400-173344800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:173331400-173370200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:173331600-173348800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr2:173331800-173348000	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr2:173332200-173344600	Strong transcription	HSMM	muscle
50	chr2:173332400-173343200	Weak transcription	Fetal Muscle Leg	muscle

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