Variant report

Variant	rs2999519
Chromosome Location	chr1:151948570-151948571
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	chr1:151948065..151950205-chr1:152058703..152061425,2	MCF-7	breast:
2	chr1:151429154..151431370-chr1:151947208..151949850,2	MCF-7	breast:

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1003107	1.00[CHB][hapmap]
rs10158030	1.00[CHB][hapmap]
rs1038746	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1038748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10788813	1.00[CHB][hapmap]
rs10788816	1.00[CHB][hapmap]
rs10888453	1.00[CHB][hapmap]
rs11204911	1.00[CHB][hapmap]
rs11204912	1.00[CHB][hapmap]
rs11204923	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11578030	1.00[CHB][hapmap]
rs12723616	1.00[CHB][hapmap]
rs1387834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1387835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473494	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1473495	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1490187	1.00[CHB][hapmap]
rs1490191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1496037	1.00[CHB][hapmap]
rs1532132	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552605	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1552606	1.00[CHB][hapmap]
rs1552607	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1602246	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1602252	0.82[ASN][1000 genomes]
rs1602254	0.82[ASN][1000 genomes]
rs17583707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1826170	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1826171	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1826172	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1844542	0.82[AMR][1000 genomes]
rs1873310	1.00[CHB][hapmap]
rs1873311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1873312	1.00[CHB][hapmap]
rs1967085	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2087550	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2338018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2338210	0.82[AMR][1000 genomes]
rs2932563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932564	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932567	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2932584	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932585	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2932588	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932596	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2932597	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999509	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2999511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999515	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999518	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999520	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999522	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999523	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2999524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999525	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999527	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2999530	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2999535	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2999536	1.00[CHB][hapmap]
rs2999537	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2999538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2999551	1.00[CHB][hapmap]
rs2999552	1.00[CHB][hapmap]
rs2999555	1.00[CHB][hapmap]
rs2999558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3001979	1.00[CHB][hapmap]
rs3007672	1.00[CHB][hapmap]
rs3007676	1.00[CHB][hapmap]
rs3007679	1.00[CHB][hapmap]
rs3007690	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap]
rs3007692	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3007693	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3007699	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3007701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3007704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3104205	1.00[CHB][hapmap]
rs3122300	1.00[CHB][hapmap]
rs3122301	1.00[CHB][hapmap]
rs3134814	1.00[CHB][hapmap]
rs34370890	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4845385	1.00[CHB][hapmap]
rs4845388	1.00[CHB][hapmap]
rs4845393	1.00[CHB][hapmap]
rs4845660	1.00[CHB][hapmap]
rs4845664	1.00[CHB][hapmap]
rs61113720	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6587626	1.00[CHB][hapmap]
rs6587628	1.00[CHB][hapmap]
rs6587629	1.00[CHB][hapmap]
rs6587630	1.00[CHB][hapmap]
rs6587641	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6659029	1.00[CHB][hapmap]
rs6685291	1.00[CHB][hapmap]
rs6691350	1.00[CHB][hapmap]
rs7529451	1.00[CHB][hapmap]
rs7532721	1.00[CHB][hapmap]
rs902314	1.00[CHB][hapmap]
rs902315	1.00[CHB][hapmap]
rs959945	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs971888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9943225	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases
6	nsv2855	chr1:151936470-151966381	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2999519	VPS72	cis	Stomach	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151934600-151953400	Weak transcription	Psoas Muscle	Psoas
2	chr1:151939600-151950800	Enhancers	Fetal Intestine Small	intestine
3	chr1:151941000-151953200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:151941000-151953200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:151941000-151953400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:151941000-151953400	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:151941000-151954800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:151941200-151952800	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:151941200-151952800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:151941200-151953000	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:151941200-151955200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:151941600-151961200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:151941800-151949400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:151941800-151953000	Weak transcription	Lung	lung
15	chr1:151941800-151953600	Weak transcription	Gastric	stomach
16	chr1:151941800-151956200	Weak transcription	Pancreas	Pancrea
17	chr1:151942400-151951800	Enhancers	Fetal Intestine Large	intestine
18	chr1:151943000-151949400	Weak transcription	Esophagus	oesophagus
19	chr1:151943000-151953000	Weak transcription	Spleen	Spleen
20	chr1:151943400-151949000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:151945400-151949200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:151945400-151952400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:151945400-151953400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:151945600-151950600	Enhancers	Duodenum Mucosa	Duodenum
25	chr1:151945600-151950800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr1:151945600-151953000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr1:151945600-151953600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:151945600-151953800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:151945600-151953800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:151946000-151949000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:151946000-151949000	Weak transcription	NH-A	brain
32	chr1:151946000-151949200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:151946000-151949200	Weak transcription	HUVEC	blood vessel
34	chr1:151946000-151949400	Weak transcription	Small Intestine	intestine
35	chr1:151946000-151949400	Weak transcription	HSMM	muscle
36	chr1:151946000-151951200	Enhancers	Hela-S3	cervix
37	chr1:151946000-151952600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:151946000-151954800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr1:151946000-151954800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:151946200-151948600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:151946200-151948800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:151946200-151949000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:151946200-151949000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr1:151946200-151949000	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:151946200-151949000	Weak transcription	Placenta	Placenta
46	chr1:151946200-151949400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:151946200-151949400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:151946200-151952800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr1:151946200-151953000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:151946200-151953000	Weak transcription	Monocytes-CD14+_RO01746	blood

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