Variant report

Variant	rs829642
Chromosome Location	chr2:30699970-30699971
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30699042..30701340-chr2:30702714..30704387,2	K562	blood:
2	chr2:30698458..30700282-chr2:30719941..30721798,2	K562	blood:

Extended variants
information (count: 79 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10167083	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs10175399	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183928	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs12053428	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs12468064	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1252624	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1252625	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1252631	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1252646	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1252651	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1252654	1.00[JPT][hapmap]
rs1525062	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs1869423	0.86[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs1869424	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs1975555	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2121600	0.86[CEU][hapmap]
rs2123753	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs2167969	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2177698	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2593442	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2593474	0.86[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs2602767	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2602808	0.86[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs2609917	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2609945	0.89[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs2692035	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4952147	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6731031	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap]
rs6740440	0.86[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap]
rs6749074	0.81[EUR][1000 genomes]
rs7583211	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs7591110	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs7592355	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829563	0.85[CEU][hapmap];0.82[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs829564	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829565	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829574	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829575	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829578	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829582	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829583	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs829618	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829622	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829630	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829632	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829634	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829641	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829653	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829654	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829659	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829662	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829663	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829664	0.85[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829669	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829670	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829671	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829672	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829677	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829679	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829681	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829682	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs829684	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829695	0.85[JPT][hapmap]
rs829696	0.81[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs829699	0.85[JPT][hapmap]
rs844194	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs860487	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs866680	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs9309680	0.88[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	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs829642	MED20	trans	brain	seeQTL
rs829642	FOSL2	cis	parietal	SCAN
rs829642	TMEM214	cis	cerebellum	SCAN
rs829642	LYCAT	cis	multi-tissue	Pritchard
rs829642	YPEL5	cis	parietal	SCAN
rs829642	EMILIN1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
4	chr2:30678600-30703800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:30678600-30710600	Weak transcription	NHLF	lung
6	chr2:30682400-30704400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:30688200-30703400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:30688400-30703400	Weak transcription	K562	blood
9	chr2:30688400-30703800	Weak transcription	Left Ventricle	heart
10	chr2:30688400-30704200	Weak transcription	Aorta	Aorta
11	chr2:30688400-30704600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:30688600-30710000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr2:30693200-30702000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:30693200-30702200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:30693600-30704000	Weak transcription	A549	lung
16	chr2:30693600-30704000	Weak transcription	HepG2	liver
17	chr2:30695200-30707000	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:30695400-30704400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:30695600-30703600	Weak transcription	GM12878-XiMat	blood
20	chr2:30695600-30704200	Weak transcription	Fetal Lung	lung
21	chr2:30695600-30705400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr2:30695800-30704000	Weak transcription	NHDF-Ad	bronchial
23	chr2:30695800-30704400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:30695800-30706600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:30696000-30701400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:30696000-30704200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:30696200-30710600	Weak transcription	Ovary	ovary
28	chr2:30696600-30703400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:30697200-30704200	Weak transcription	Fetal Intestine Large	intestine
30	chr2:30697400-30710400	Weak transcription	Fetal Kidney	kidney
31	chr2:30697800-30704200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
33	chr2:30698000-30708000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr2:30698000-30709400	Weak transcription	Pancreas	Pancrea
35	chr2:30698200-30704200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:30698200-30704200	Weak transcription	Right Atrium	heart
37	chr2:30698200-30704400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:30698200-30710600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr2:30698400-30700400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:30698400-30706800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr2:30698600-30704400	Weak transcription	Primary B cells from cord blood	blood
42	chr2:30698800-30700000	Enhancers	Fetal Heart	heart
43	chr2:30699000-30702200	Weak transcription	Primary T cells from cord blood	blood
44	chr2:30699000-30702200	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr2:30699000-30704000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr2:30699000-30709600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr2:30699000-30711800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:30699600-30709400	Weak transcription	Right Ventricle	heart
49	chr2:30699800-30704200	Weak transcription	Psoas Muscle	Psoas

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