Variant report

Variant	rs1574259
Chromosome Location	chr2:173313453-173313454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1001926	1.00[AFR][1000 genomes]
rs10187564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10207640	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10207654	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10210544	0.86[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10803874	1.00[CEU][hapmap]
rs10930559	1.00[CEU][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12052253	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052385	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12053442	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12613307	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12615584	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12615596	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620581	1.00[CEU][hapmap]
rs12621278	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622724	1.00[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13387602	0.85[ASN][1000 genomes]
rs13410475	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13414928	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13421350	0.81[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1574256	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860397	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16860416	0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs16860419	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16860426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16860438	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16860478	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16860497	1.00[CEU][hapmap]
rs16860513	1.00[CEU][hapmap]
rs16860515	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16860634	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs2008518	1.00[AFR][1000 genomes]
rs2178476	1.00[AFR][1000 genomes]
rs2272496	1.00[AFR][1000 genomes]
rs2293645	1.00[CEU][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.85[EUR][1000 genomes]
rs2293647	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[AFR][1000 genomes]
rs2293648	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs28485589	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3762618	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4405725	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55867175	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56882727	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs56892098	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57244773	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57404607	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57587465	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs57878744	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59374567	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs59454075	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59970483	0.85[EUR][1000 genomes]
rs60096331	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6726739	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs6730284	0.85[EUR][1000 genomes]
rs6741759	0.85[EUR][1000 genomes]
rs7564416	0.86[JPT][hapmap]
rs9636257	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1574259	UHRF1BP1	trans	brain	seeQTL
rs1574259	TCTEX1D1	trans	brain	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173305000-173316800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:173306800-173316400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:173307200-173318600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:173307400-173313600	Weak transcription	Placenta	Placenta
5	chr2:173307400-173322400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:173307600-173313600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:173307600-173313800	Weak transcription	Right Ventricle	heart
8	chr2:173307600-173314000	Enhancers	Duodenum Mucosa	Duodenum
9	chr2:173307600-173314600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:173307600-173314800	Weak transcription	Esophagus	oesophagus
11	chr2:173307600-173315600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:173307600-173321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:173308000-173313800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:173309000-173317000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:173309200-173315200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:173309400-173315600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:173310400-173314600	Enhancers	HMEC	breast
18	chr2:173310400-173318000	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:173310600-173314400	Enhancers	Fetal Intestine Small	intestine
20	chr2:173310600-173314600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:173310800-173313600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:173310800-173313600	Weak transcription	Left Ventricle	heart
23	chr2:173310800-173313600	Weak transcription	Right Atrium	heart
24	chr2:173310800-173314200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:173310800-173314600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:173310800-173314800	Weak transcription	Psoas Muscle	Psoas
27	chr2:173310800-173314800	Weak transcription	Spleen	Spleen
28	chr2:173310800-173317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:173310800-173318200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:173310800-173318600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:173310800-173319800	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:173310800-173320000	Weak transcription	Lung	lung
33	chr2:173310800-173322400	Weak transcription	Thymus	Thymus
34	chr2:173311000-173316400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr2:173311400-173313600	Weak transcription	Gastric	stomach
36	chr2:173311400-173314000	Enhancers	Pancreas	Pancrea
37	chr2:173311400-173314400	Enhancers	Fetal Intestine Large	intestine
38	chr2:173311400-173315000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:173311400-173318000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr2:173311600-173314800	Weak transcription	NH-A	brain
41	chr2:173311600-173314800	Enhancers	NHEK	skin
42	chr2:173311600-173316000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:173311600-173316400	Weak transcription	Adipose Nuclei	Adipose
44	chr2:173311600-173317200	Weak transcription	Liver	Liver
45	chr2:173311600-173319000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:173311600-173319200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:173311600-173319200	Weak transcription	HUVEC	blood vessel
48	chr2:173311800-173314200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr2:173311800-173317200	Weak transcription	Fetal Thymus	thymus
50	chr2:173311800-173319200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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