Variant report

Variant	rs4696290
Chromosome Location	chr4:152631472-152631473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152618119..152619775-chr4:152630360..152632137,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10001603	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10013612	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10016160	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10222838	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10222925	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11099828	0.87[ASN][1000 genomes]
rs11099829	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11723227	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12331037	0.85[GIH][hapmap]
rs12502446	0.86[ASN][1000 genomes]
rs12503677	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12506000	0.82[ASN][1000 genomes]
rs12641433	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12641438	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12641441	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12645029	0.80[EUR][1000 genomes]
rs12647420	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12647462	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12647465	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12647616	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13108359	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13119490	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13147021	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1366907	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1397683	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1429558	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1429559	0.81[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17360475	0.85[GIH][hapmap]
rs1877185	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877186	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1877188	0.92[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2007218	0.87[GIH][hapmap]
rs2089811	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2175409	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303866	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2406973	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.81[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2406974	0.88[EUR][1000 genomes]
rs28659854	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749561	0.85[GIH][hapmap]
rs3792691	0.87[GIH][hapmap]
rs3805356	0.81[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3828546	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4554052	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4643789	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696106	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4696107	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696108	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696109	0.85[GIH][hapmap]
rs4696110	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4696286	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4696287	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4696288	0.83[EUR][1000 genomes]
rs4696289	0.83[EUR][1000 genomes]
rs4696293	0.81[GIH][hapmap]
rs4696295	0.92[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4696297	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58751443	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59350867	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62327349	0.83[EUR][1000 genomes]
rs62327350	0.82[EUR][1000 genomes]
rs6535816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6535818	0.85[GIH][hapmap]
rs6535819	0.85[GIH][hapmap]
rs6535822	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6816002	0.88[EUR][1000 genomes]
rs6847844	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6849111	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6855883	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6857073	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7654294	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7669465	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7669761	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7669977	0.85[GIH][hapmap]
rs7675818	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs867800	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9996320	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[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	nsv508322	chr4:152617079-152678951	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4696290	PET112L	cis	parietal	SCAN
rs4696290	FAM160A1	cis	cerebellum	SCAN
rs4696290	PET112L	cis	lymphoblastoid	seeQTL
rs4696290	PET112L	cis	cerebellum	SCAN
rs4696290	PET112L	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152585800-152640400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr4:152591200-152646800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:152592600-152636400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:152596400-152640600	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr4:152598400-152648200	Weak transcription	HMEC	breast
6	chr4:152599000-152637200	Weak transcription	GM12878-XiMat	blood
7	chr4:152609200-152640200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr4:152609600-152640400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr4:152609800-152646200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:152611800-152640000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:152612000-152651000	Weak transcription	K562	blood
12	chr4:152612200-152632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:152612400-152631800	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr4:152612400-152642600	Weak transcription	NHLF	lung
15	chr4:152614400-152640200	Weak transcription	Gastric	stomach
16	chr4:152614600-152651200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:152615000-152651000	Weak transcription	HSMM	muscle
18	chr4:152616600-152665400	Weak transcription	NHDF-Ad	bronchial
19	chr4:152619000-152638400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:152620400-152632400	Weak transcription	Psoas Muscle	Psoas
21	chr4:152620600-152641200	Strong transcription	Primary T cells from cord blood	blood
22	chr4:152621400-152651600	Weak transcription	Small Intestine	intestine
23	chr4:152622000-152644600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:152622400-152640000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr4:152622600-152641000	Weak transcription	HSMMtube	muscle
26	chr4:152622800-152638000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:152623000-152646200	Weak transcription	Fetal Lung	lung
28	chr4:152623200-152648200	Weak transcription	NHEK	skin
29	chr4:152623400-152639600	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr4:152623800-152634800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr4:152623800-152642600	Weak transcription	Fetal Kidney	kidney
32	chr4:152624000-152635600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:152624000-152645600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr4:152624000-152646400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr4:152624200-152638600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:152624200-152639800	Weak transcription	Placenta	Placenta
37	chr4:152625000-152635000	Weak transcription	Brain Angular Gyrus	brain
38	chr4:152625000-152651000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr4:152625200-152634800	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr4:152625200-152635400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr4:152625200-152642400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:152625600-152640200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:152626600-152634200	Weak transcription	Brain Anterior Caudate	brain
44	chr4:152627200-152634800	Weak transcription	Fetal Thymus	thymus
45	chr4:152627400-152641200	Weak transcription	Right Ventricle	heart
46	chr4:152629000-152640200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr4:152629000-152658800	Weak transcription	Pancreas	Pancrea
48	chr4:152629200-152632400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:152629200-152636200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:152629200-152637600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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