Variant report

Variant	rs947270
Chromosome Location	chr1:120337384-120337385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120324473..120326821-chr1:120335135..120337895,2	K562	blood:
2	chr1:120327792..120331105-chr1:120334813..120337801,3	MCF-7	breast:
3	chr1:120336862..120340464-chr1:120344663..120347846,4	MCF-7	breast:
4	chr1:120315709..120317268-chr1:120336953..120338874,2	MCF-7	breast:
5	chr1:120329924..120336261-chr1:120336777..120341772,6	K562	blood:
6	chr1:120290151..120293053-chr1:120335824..120338207,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10494231	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1052972	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737757	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10737758	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737759	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737760	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10754420	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10754421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10754422	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754423	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10754424	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10754425	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10802134	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802135	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802136	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10802137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10923900	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10923902	0.90[EUR][1000 genomes]
rs10923903	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923904	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923905	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1163545	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12047532	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566808	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12567027	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12567029	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12730035	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12747679	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441006	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441007	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441013	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530227	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539071	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539074	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539075	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17258467	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2119470	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282403	0.93[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2289458	0.84[EUR][1000 genomes]
rs2582783	0.82[JPT][hapmap]
rs2793836	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4659236	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4659237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6428841	0.85[CEU][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs6428842	0.80[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6428843	0.85[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6661517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683871	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6689072	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697347	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698813	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698907	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs699778	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs729234	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7516324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs753424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs935056	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935057	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs935059	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];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:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv915933	chr1:120323527-120471049	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv831226	chr1:120331599-120471049	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs947270	HMGCS2	cis	lung	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120331000-120337800	Weak transcription	HMEC	breast
2	chr1:120332800-120341600	Enhancers	Fetal Stomach	stomach
3	chr1:120333800-120339200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:120334000-120338400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:120334000-120339400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:120334200-120338000	Weak transcription	Small Intestine	intestine
7	chr1:120334600-120337800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:120334800-120337400	Weak transcription	Fetal Kidney	kidney
9	chr1:120335800-120338800	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr1:120336000-120338600	Enhancers	Fetal Muscle Leg	muscle
11	chr1:120336000-120338800	Enhancers	Fetal Intestine Large	intestine
12	chr1:120336000-120338800	Enhancers	Stomach Mucosa	stomach
13	chr1:120336000-120340200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:120336000-120341600	Weak transcription	Primary T cells from cord blood	blood
15	chr1:120336000-120349400	Weak transcription	Right Atrium	heart
16	chr1:120336200-120338800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:120336200-120339600	Enhancers	Colon Smooth Muscle	Colon
18	chr1:120336400-120338000	Flanking Active TSS	Stomach Smooth Muscle	stomach
19	chr1:120336400-120338400	Enhancers	Gastric	stomach
20	chr1:120336400-120342200	Weak transcription	Spleen	Spleen
21	chr1:120336600-120337800	Weak transcription	Placenta	Placenta
22	chr1:120336600-120338000	Weak transcription	Esophagus	oesophagus
23	chr1:120336600-120338000	Enhancers	HepG2	liver
24	chr1:120336600-120338200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:120336800-120337800	Weak transcription	Pancreas	Pancrea
26	chr1:120336800-120338200	Enhancers	Osteobl	bone
27	chr1:120337000-120337400	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr1:120337000-120338000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:120337000-120338200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:120337000-120338400	Enhancers	Liver	Liver
31	chr1:120337000-120338600	Enhancers	Colonic Mucosa	Colon
32	chr1:120337000-120338800	Enhancers	Duodenum Mucosa	Duodenum
33	chr1:120337000-120340000	Enhancers	Fetal Lung	lung
34	chr1:120337200-120337800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:120337200-120338000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:120337200-120339600	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:120337200-120340000	Enhancers	Fetal Intestine Small	intestine

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