Variant report

Variant	rs9868257
Chromosome Location	chr3:121715319-121715320
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:121573144..121575640-chr3:121713880..121715602,2	MCF-7	breast:
2	chr3:121707943..121710832-chr3:121713197..121716024,2	MCF-7	breast:
3	chr3:121574042..121575089-chr3:121714066..121715464,7	MCF-7	breast:

Extended variants
information (count: 127 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10934562	0.82[EUR][1000 genomes]
rs10934569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10934570	0.86[CHB][hapmap]
rs1143670	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1143671	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs1143672	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs11718322	0.84[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11914993	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs11920521	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs11920547	0.82[EUR][1000 genomes]
rs11924058	0.87[EUR][1000 genomes]
rs11929195	0.81[CHB][hapmap]
rs11929235	0.81[CHB][hapmap]
rs1316301	0.83[EUR][1000 genomes]
rs1316397	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs1357531	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs1523517	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1881999	0.83[EUR][1000 genomes]
rs1882000	0.83[EUR][1000 genomes]
rs1882002	0.83[EUR][1000 genomes]
rs1882003	0.83[EUR][1000 genomes]
rs1882004	0.82[EUR][1000 genomes]
rs1920302	0.82[EUR][1000 genomes]
rs1920317	0.83[EUR][1000 genomes]
rs1920318	0.83[EUR][1000 genomes]
rs1920319	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2001212	0.82[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2049330	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2049331	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2141615	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2178415	0.82[EUR][1000 genomes]
rs2257109	0.82[EUR][1000 genomes]
rs2257115	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2257119	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2257120	0.82[EUR][1000 genomes]
rs2257123	0.82[EUR][1000 genomes]
rs2257124	0.82[EUR][1000 genomes]
rs2257132	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2257212	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2257214	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2262494	0.83[EUR][1000 genomes]
rs2293612	0.83[EUR][1000 genomes]
rs2293614	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs2293615	0.83[EUR][1000 genomes]
rs2293616	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2332032	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2332036	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2332044	0.82[EUR][1000 genomes]
rs2332046	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs2332049	0.82[EUR][1000 genomes]
rs2332050	0.82[EUR][1000 genomes]
rs2332051	0.82[EUR][1000 genomes]
rs2332052	0.81[EUR][1000 genomes]
rs2332053	0.82[EUR][1000 genomes]
rs2332054	0.82[EUR][1000 genomes]
rs2689272	0.82[EUR][1000 genomes]
rs2689273	0.82[EUR][1000 genomes]
rs2689281	0.82[EUR][1000 genomes]
rs2689282	0.82[EUR][1000 genomes]
rs2689283	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2689284	0.82[EUR][1000 genomes]
rs2689287	0.83[EUR][1000 genomes]
rs2689288	0.83[EUR][1000 genomes]
rs2689289	0.82[EUR][1000 genomes]
rs2689291	0.82[EUR][1000 genomes]
rs2689292	0.82[EUR][1000 genomes]
rs2700416	0.82[EUR][1000 genomes]
rs2700420	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2700421	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes]
rs2700425	0.83[EUR][1000 genomes]
rs2700426	0.82[EUR][1000 genomes]
rs2877566	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2877568	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs2877569	0.82[EUR][1000 genomes]
rs3762819	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs3762821	0.84[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs3762822	0.83[EUR][1000 genomes]
rs3792596	0.82[EUR][1000 genomes]
rs3792597	0.83[EUR][1000 genomes]
rs3805134	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs3805138	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs3817601	0.83[EUR][1000 genomes]
rs3915061	0.87[CHB][hapmap]
rs3932367	0.80[EUR][1000 genomes]
rs4583698	0.83[EUR][1000 genomes]
rs4974395	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4974396	0.95[ASN][1000 genomes]
rs4974397	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59823080	0.81[EUR][1000 genomes]
rs6438687	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs6765799	0.82[EUR][1000 genomes]
rs6791876	0.82[EUR][1000 genomes]
rs6794360	0.81[EUR][1000 genomes]
rs6803757	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs7635449	0.82[EUR][1000 genomes]
rs7637569	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs866926	0.88[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs866927	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs866929	0.82[EUR][1000 genomes]
rs874741	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs874742	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs9289181	0.81[EUR][1000 genomes]
rs9289182	0.88[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs9289183	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9811473	0.82[EUR][1000 genomes]
rs9812515	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs9815756	0.82[EUR][1000 genomes]
rs9816071	0.82[EUR][1000 genomes]
rs9816215	0.82[EUR][1000 genomes]
rs9816720	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9822474	0.82[EUR][1000 genomes]
rs9827390	0.82[EUR][1000 genomes]
rs9828753	0.82[EUR][1000 genomes]
rs9829070	0.82[EUR][1000 genomes]
rs9830721	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs9835875	0.82[EUR][1000 genomes]
rs9836339	0.82[EUR][1000 genomes]
rs9845790	0.81[EUR][1000 genomes]
rs9850685	0.82[EUR][1000 genomes]
rs9856253	0.81[EUR][1000 genomes]
rs9862977	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs9863155	0.82[EUR][1000 genomes]
rs9866936	0.82[EUR][1000 genomes]
rs9867460	0.84[EUR][1000 genomes]
rs9870245	0.83[EUR][1000 genomes]
rs9871534	0.82[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	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9868257	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs9868257	SLC15A2	cis	Heart Left Ventricle	GTEx
rs9868257	SLC15A2	cis	Muscle Skeletal	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121704800-121721400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:121706000-121721200	Weak transcription	Fetal Kidney	kidney
4	chr3:121708800-121718000	Enhancers	Primary B cells from peripheral blood	blood
5	chr3:121709200-121719200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:121709600-121721800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:121711600-121715400	Enhancers	Spleen	Spleen
8	chr3:121712200-121718800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:121712800-121716000	Weak transcription	Fetal Intestine Large	intestine
10	chr3:121712800-121721600	Weak transcription	Colonic Mucosa	Colon
11	chr3:121713000-121732200	Weak transcription	Esophagus	oesophagus
12	chr3:121713200-121717800	Enhancers	Adipose Nuclei	Adipose
13	chr3:121713200-121719000	Enhancers	HUVEC	blood vessel
14	chr3:121713400-121718600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:121713400-121718800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr3:121713600-121715400	Enhancers	Fetal Muscle Leg	muscle
17	chr3:121713600-121715400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:121713600-121716800	Enhancers	Placenta	Placenta
19	chr3:121713800-121718400	Enhancers	Primary B cells from cord blood	blood
20	chr3:121714000-121715400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:121714000-121715400	Enhancers	HSMM	muscle
22	chr3:121714000-121715600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:121714000-121715800	Enhancers	HMEC	breast
24	chr3:121714000-121716800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr3:121714000-121717400	Enhancers	NHEK	skin
26	chr3:121714000-121718000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:121714200-121715400	Enhancers	Fetal Thymus	thymus
28	chr3:121714200-121717400	Weak transcription	Right Atrium	heart
29	chr3:121714200-121717800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:121714400-121715400	Enhancers	Brain Substantia Nigra	brain
31	chr3:121714400-121716800	Weak transcription	NHLF	lung
32	chr3:121714400-121717200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr3:121714400-121719800	Weak transcription	Lung	lung
34	chr3:121714600-121716200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:121714600-121717000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:121714600-121719200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr3:121714800-121716200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:121714800-121716200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr3:121714800-121716200	Weak transcription	Fetal Intestine Small	intestine
40	chr3:121714800-121716200	Weak transcription	Pancreas	Pancrea
41	chr3:121714800-121716800	Weak transcription	NHDF-Ad	bronchial
42	chr3:121714800-121717200	Weak transcription	Hela-S3	cervix
43	chr3:121714800-121717400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr3:121714800-121719400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr3:121714800-121719600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:121714800-121720000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:121715000-121716200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:121715000-121716200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:121715000-121716200	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr3:121715000-121716200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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