Variant report

Variant	rs4665140
Chromosome Location	chr2:160890710-160890711
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:160886980..160889111-chr2:160890528..160892993,3	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10497205	1.00[YRI][hapmap]
rs10497209	1.00[YRI][hapmap]
rs10497210	1.00[YRI][hapmap]
rs10497213	0.86[JPT][hapmap]
rs10929965	0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs10929966	0.80[ASN][1000 genomes]
rs13001911	0.82[JPT][hapmap]
rs1511218	0.80[ASN][1000 genomes]
rs16844715	1.00[YRI][hapmap]
rs16844848	0.81[JPT][hapmap]
rs16844863	0.81[JPT][hapmap]
rs16844866	0.82[JPT][hapmap]
rs17216980	0.86[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17218566	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs17231342	1.00[YRI][hapmap]
rs17231993	1.00[YRI][hapmap]
rs17241282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17341301	0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs17828159	1.00[YRI][hapmap]
rs17829873	1.00[YRI][hapmap]
rs17830307	1.00[YRI][hapmap]
rs17830558	1.00[YRI][hapmap]
rs17830755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17830904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17830940	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17831161	0.91[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs17831191	0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs17831251	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs2124969	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs2175416	1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs2198918	0.82[JPT][hapmap]
rs2221808	1.00[YRI][hapmap]
rs2305818	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs2305819	0.81[JPT][hapmap]
rs34248629	0.80[ASN][1000 genomes]
rs35771982	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749114	1.00[YRI][hapmap]
rs3749117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749119	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs3792168	1.00[YRI][hapmap]
rs3792175	1.00[YRI][hapmap]
rs3792192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828324	1.00[YRI][hapmap]
rs4292050	0.87[JPT][hapmap];1.00[YRI][hapmap]
rs4664308	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4665138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4665147	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs4665161	0.82[JPT][hapmap]
rs4665162	0.82[JPT][hapmap];1.00[YRI][hapmap]
rs55668231	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59137532	0.93[ASN][1000 genomes]
rs62175487	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62175488	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62175515	0.80[ASN][1000 genomes]
rs66484345	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66667042	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705574	0.88[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6707458	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs6719686	0.90[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs6722275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6731260	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs6732107	0.82[JPT][hapmap]
rs6739867	0.86[JPT][hapmap];1.00[YRI][hapmap]
rs6759836	0.83[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6759924	1.00[YRI][hapmap]
rs877200	0.82[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs925410	0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs979129	1.00[YRI][hapmap]
rs983916	1.00[YRI][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4665140	LY75	cis	Thyroid	GTEx
rs4665140	LY75	cis	Skin Sun Exposed Lower leg	GTEx
rs4665140	LY75	cis	Esophagus Mucosa	GTEx
rs4665140	LY75	cis	lung	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:160828600-160907200	Weak transcription	Small Intestine	intestine
2	chr2:160862800-160899600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:160867600-160893800	Weak transcription	HMEC	breast
4	chr2:160876800-160895800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:160879400-160908000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:160879800-160896200	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:160879800-160907800	Weak transcription	NHEK	skin
8	chr2:160881200-160912000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:160881200-160913400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:160881600-160898400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr2:160881600-160900800	Weak transcription	Spleen	Spleen
12	chr2:160881600-160902000	Weak transcription	Esophagus	oesophagus
13	chr2:160883000-160893600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr2:160883600-160891000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:160884000-160911600	Weak transcription	Fetal Kidney	kidney
16	chr2:160885400-160895800	Weak transcription	Fetal Stomach	stomach
17	chr2:160885400-160895800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:160885600-160893600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:160885600-160896800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:160885800-160892800	Weak transcription	Aorta	Aorta
21	chr2:160885800-160893000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:160885800-160896200	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:160886000-160891000	Weak transcription	Left Ventricle	heart
24	chr2:160886000-160893000	Weak transcription	Fetal Intestine Small	intestine
25	chr2:160886000-160893000	Weak transcription	Ovary	ovary
26	chr2:160886000-160893400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:160886000-160894000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:160886000-160901400	Weak transcription	Lung	lung
29	chr2:160888000-160902800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:160888600-160891000	Weak transcription	Fetal Intestine Large	intestine
31	chr2:160889000-160891400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:160889600-160891400	Enhancers	HUVEC	blood vessel
33	chr2:160889600-160891400	Enhancers	Osteobl	bone
34	chr2:160889800-160891400	Enhancers	Muscle Satellite Cultured Cells	--
35	chr2:160890000-160891200	Enhancers	HSMM	muscle
36	chr2:160890000-160891200	Enhancers	NH-A	brain
37	chr2:160890000-160892000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:160890000-160892000	Enhancers	Adipose Nuclei	Adipose
39	chr2:160890200-160891200	Enhancers	A549	lung
40	chr2:160890200-160891200	Enhancers	NHLF	lung
41	chr2:160890200-160891400	Enhancers	NHDF-Ad	bronchial
42	chr2:160890400-160891200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr2:160890400-160891400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:160890600-160892000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:160890600-160892000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:160890600-160892000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr2:160890600-160893800	Weak transcription	HSMMtube	muscle
48	chr2:160890600-160907800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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