Variant report

Variant	rs4237189
Chromosome Location	chr9:100083953-100083954
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100075658..100077639-chr9:100081939..100084520,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10122063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10125198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1020884	0.88[EUR][1000 genomes]
rs1020885	0.88[EUR][1000 genomes]
rs1037948	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1037950	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1037951	0.87[EUR][1000 genomes]
rs10435867	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10435868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10448274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10759527	0.85[CEU][hapmap]
rs10759624	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10759657	0.88[EUR][1000 genomes]
rs10817273	0.86[CEU][hapmap]
rs10817286	0.86[CEU][hapmap]
rs10817487	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10981280	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10981288	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10981296	0.89[YRI][hapmap]
rs10981329	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10981438	0.81[ASN][1000 genomes]
rs10981890	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981919	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs10981931	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11581	0.86[JPT][hapmap]
rs11791310	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12235305	0.81[ASN][1000 genomes]
rs13298346	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13299627	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1542506	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs1544203	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs1903635	0.81[JPT][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1947717	0.92[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2169456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2219664	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2242187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2279114	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2306097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2493442	0.81[ASN][1000 genomes]
rs2493443	0.86[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2502644	0.88[JPT][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2615143	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2615145	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2795365	0.81[ASN][1000 genomes]
rs2795367	0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2818238	0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs2818243	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3214072	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs34955252	0.80[ASN][1000 genomes]
rs35609998	0.80[ASN][1000 genomes]
rs3747489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3747493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3747496	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3802471	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4313271	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4366181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4523384	0.80[ASN][1000 genomes]
rs4523385	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4554595	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742685	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4742689	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs4742690	0.88[EUR][1000 genomes]
rs4743072	0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4743076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4743084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743087	0.96[CEU][hapmap]
rs4743088	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6478095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6478131	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7020393	0.91[JPT][hapmap]
rs7042707	0.91[JPT][hapmap]
rs713066	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs750674	0.96[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7856924	0.89[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7869536	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9696167	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[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	esv2762823	chr9:100083872-100105782	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4237189	VN1R51P	cis	Thyroid	GTEx
rs4237189	RP11-520B13.4	cis	Esophagus Muscularis	GTEx
rs4237189	ANKRD18CP	cis	Thyroid	GTEx
rs4237189	RP11-498P14.5	cis	lung	GTEx
rs4237189	RP11-520B13.4	cis	Thyroid	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100069400-100092800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr9:100069600-100094400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr9:100069800-100086400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:100070000-100091400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:100070000-100093800	Weak transcription	Psoas Muscle	Psoas
6	chr9:100070000-100098000	Weak transcription	Small Intestine	intestine
7	chr9:100070000-100100200	Weak transcription	Fetal Heart	heart
8	chr9:100070000-100131400	Weak transcription	Fetal Kidney	kidney
9	chr9:100070200-100092600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr9:100070200-100095000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:100070400-100091800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:100070400-100092800	Weak transcription	Colonic Mucosa	Colon
13	chr9:100070400-100095200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:100070600-100089600	Weak transcription	Osteobl	bone
15	chr9:100071000-100094400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:100071200-100093000	Strong transcription	Stomach Smooth Muscle	stomach
17	chr9:100071600-100084000	Strong transcription	Fetal Muscle Leg	muscle
18	chr9:100071600-100088800	Strong transcription	Brain Germinal Matrix	brain
19	chr9:100071600-100089200	Strong transcription	Fetal Intestine Small	intestine
20	chr9:100071600-100093000	Strong transcription	Fetal Stomach	stomach
21	chr9:100071600-100093400	Strong transcription	Brain Anterior Caudate	brain
22	chr9:100071600-100093800	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr9:100071600-100093800	Strong transcription	Ovary	ovary
24	chr9:100071600-100094600	Strong transcription	Brain Angular Gyrus	brain
25	chr9:100071800-100084400	Strong transcription	Aorta	Aorta
26	chr9:100071800-100093400	Strong transcription	Adipose Nuclei	Adipose
27	chr9:100071800-100093600	Strong transcription	Left Ventricle	heart
28	chr9:100073000-100089200	Strong transcription	Brain Hippocampus Middle	brain
29	chr9:100075200-100085000	Weak transcription	Esophagus	oesophagus
30	chr9:100075600-100089600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr9:100076000-100093200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr9:100076000-100093600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:100076200-100092400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr9:100077000-100106400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr9:100077000-100140800	Weak transcription	Fetal Brain Male	brain
36	chr9:100078000-100084200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:100078000-100087800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr9:100078000-100089000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:100078000-100091800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr9:100078200-100084600	Weak transcription	K562	blood
41	chr9:100078200-100091800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:100078400-100085000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:100078400-100087400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr9:100078400-100092800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr9:100078600-100085400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr9:100078800-100085000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr9:100079000-100085000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:100079400-100084000	Weak transcription	Pancreas	Pancrea
49	chr9:100079400-100089600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:100079600-100084000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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