Variant report

Variant	rs1252646
Chromosome Location	chr2:30741913-30741914
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:30740997..30743225-chr2:30749540..30752188,2	MCF-7	breast:
2	chr2:30739882..30742523-chr2:30744802..30747234,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10167083	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs10175399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs10183928	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs12053428	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs12468064	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1252624	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1252625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1252631	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1252651	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1252654	1.00[JPT][hapmap]
rs1525062	0.93[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs1869423	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs1869424	0.93[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap]
rs1975555	0.93[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2121600	0.93[CEU][hapmap]
rs2123753	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs2167969	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2177698	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs2593442	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs2593474	0.93[CEU][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs2602767	0.93[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2602808	0.93[CEU][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs2609917	0.93[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs2609945	0.86[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs2692035	0.85[EUR][1000 genomes]
rs4952147	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6731031	0.93[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap]
rs6740440	0.93[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs6749074	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7583211	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs7591110	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs7592355	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829563	0.92[CEU][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap]
rs829564	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829565	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829574	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829575	1.00[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];0.89[EUR][1000 genomes]
rs829578	0.89[EUR][1000 genomes]
rs829582	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829583	0.85[EUR][1000 genomes]
rs829618	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829619	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829620	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829622	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829630	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829631	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829632	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829641	1.00[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];0.89[EUR][1000 genomes]
rs829642	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]
rs829646	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829653	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829654	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829655	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829659	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829661	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829662	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829663	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829664	0.92[CEU][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829665	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs829670	0.83[EUR][1000 genomes]
rs829671	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829672	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829673	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829675	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]
rs829677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs829680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829681	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829682	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs829684	0.93[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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs860486	0.81[EUR][1000 genomes]
rs860487	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs866680	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs9309680	0.93[EUR][1000 genomes];0.92[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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1252646	MED20	trans	brain	seeQTL
rs1252646	RSAD1	trans	brain	seeQTL
rs1252646	FOSL2	cis	parietal	SCAN
rs1252646	LYCAT	cis	multi-tissue	Pritchard
rs1252646	TMEM214	cis	cerebellum	SCAN
rs1252646	EMILIN1	cis	parietal	SCAN
rs1252646	YPEL5	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30726200-30742600	Weak transcription	Pancreas	Pancrea
2	chr2:30729000-30764600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr2:30732800-30742000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:30733000-30756000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:30734800-30742200	Weak transcription	Gastric	stomach
6	chr2:30734800-30764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:30735000-30742600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:30735000-30742600	Weak transcription	HSMMtube	muscle
9	chr2:30735400-30742200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:30735400-30742200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:30735400-30742600	Weak transcription	Fetal Intestine Large	intestine
12	chr2:30735600-30742800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:30736800-30752400	Weak transcription	Psoas Muscle	Psoas
14	chr2:30737000-30742400	Weak transcription	Left Ventricle	heart
15	chr2:30737600-30742000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr2:30737800-30742600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:30738000-30742200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:30738000-30742600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:30738000-30742600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:30738000-30742600	Weak transcription	NHEK	skin
21	chr2:30738000-30750400	Weak transcription	Liver	Liver
22	chr2:30738000-30757000	Weak transcription	Ovary	ovary
23	chr2:30738200-30742600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:30738200-30742600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:30738200-30742600	Weak transcription	NHLF	lung
26	chr2:30738200-30742800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr2:30738200-30744000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr2:30738200-30750000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:30738200-30750800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:30738200-30750800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr2:30738200-30751000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:30738200-30752400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:30738200-30758200	Weak transcription	Right Ventricle	heart
34	chr2:30738400-30742000	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:30738400-30742200	Weak transcription	Fetal Stomach	stomach
36	chr2:30738400-30748600	Weak transcription	Fetal Kidney	kidney
37	chr2:30738400-30756200	Weak transcription	Hela-S3	cervix
38	chr2:30739000-30742200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
39	chr2:30739000-30742400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:30739400-30742000	Weak transcription	Fetal Lung	lung
41	chr2:30739400-30742200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr2:30739600-30742000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:30740200-30742600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:30741000-30745200	Weak transcription	Fetal Heart	heart
45	chr2:30741200-30743000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
46	chr2:30741400-30743000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:30741400-30743000	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:30741400-30743400	ZNF genes & repeats	Primary T cells from cord blood	blood
49	chr2:30741400-30743400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:30741400-30743600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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