Variant report

Variant	rs3818433
Chromosome Location	chr1:179079190-179079191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179075971..179079448-chr1:179095385..179098448,3	MCF-7	breast:
2	chr1:179072158..179075284-chr1:179075510..179079564,3	K562	blood:
3	chr1:179076910..179079284-chr1:179198246..179199941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143322	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1046385	1.00[ASW][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap]
rs1078872	0.88[GIH][hapmap]
rs10798652	0.81[JPT][hapmap]
rs10913690	0.88[GIH][hapmap]
rs10913691	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913697	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs1173077	0.95[GIH][hapmap];0.80[TSI][hapmap]
rs12022539	0.95[CEU][hapmap]
rs12049237	0.95[CEU][hapmap]
rs12130276	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs12402165	0.95[CEU][hapmap]
rs12408349	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];0.82[MEX][hapmap]
rs1325194	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17362081	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1856968	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs2025582	1.00[LWK][hapmap]
rs2050922	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2066162	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2130576	0.93[GIH][hapmap]
rs2171959	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs2296377	0.83[AMR][1000 genomes]
rs2493124	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs2636266	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs2636274	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs2636276	0.88[GIH][hapmap];0.80[TSI][hapmap]
rs2636278	0.88[CHB][hapmap];0.88[CHD][hapmap]
rs2636280	0.93[GIH][hapmap]
rs2636289	0.90[EUR][1000 genomes]
rs2636290	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2791941	0.88[GIH][hapmap];0.80[TSI][hapmap]
rs2793791	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2793796	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs2793797	0.93[GIH][hapmap];0.80[TSI][hapmap]
rs2793799	0.95[GIH][hapmap];0.80[TSI][hapmap]
rs2793804	0.89[EUR][1000 genomes]
rs2793805	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs2793807	0.90[EUR][1000 genomes]
rs2793808	0.90[EUR][1000 genomes]
rs2793812	0.90[GIH][hapmap]
rs2793816	0.88[GIH][hapmap]
rs2816179	0.80[EUR][1000 genomes]
rs2816203	0.93[GIH][hapmap]
rs2816209	0.97[GIH][hapmap];0.80[TSI][hapmap]
rs2816213	0.93[GIH][hapmap]
rs3210839	0.92[GIH][hapmap]
rs380951	0.86[EUR][1000 genomes]
rs3813638	1.00[ASW][hapmap]
rs3813642	0.88[GIH][hapmap]
rs3813643	0.88[GIH][hapmap]
rs425858	0.86[EUR][1000 genomes]
rs4478776	0.86[EUR][1000 genomes]
rs451088	0.90[GIH][hapmap]
rs4651014	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61821690	0.90[EUR][1000 genomes]
rs6425512	1.00[ASW][hapmap]
rs7544801	1.00[ASW][hapmap]
rs915337	0.90[GIH][hapmap]
rs931441	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs9728480	0.93[GIH][hapmap];0.80[TSI][hapmap]

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	nsv1002511	chr1:179077914-179089842	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3818433	LHX4	cis	parietal	SCAN
rs3818433	ABL2	cis	parietal	SCAN
rs3818433	IER5	cis	cerebellum	SCAN
rs3818433	TOR3A	cis	Artery Tibial	GTEx
rs3818433	TOR3A	cis	multi-tissue	Pritchard
rs3818433	ABL2	cis	cerebellum	SCAN
rs3818433	FAM20B	cis	parietal	SCAN
rs3818433	RALGPS2	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179053200-179096000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:179054000-179079400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr1:179059200-179096400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:179059400-179090400	Strong transcription	HUVEC	blood vessel
5	chr1:179061400-179090400	Strong transcription	HSMM	muscle
6	chr1:179062000-179088000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:179063200-179112000	Weak transcription	Fetal Kidney	kidney
8	chr1:179064800-179079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:179064800-179097800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:179069400-179080400	Strong transcription	HMEC	breast
11	chr1:179070400-179087200	Weak transcription	Psoas Muscle	Psoas
12	chr1:179071400-179090400	Strong transcription	NHDF-Ad	bronchial
13	chr1:179072000-179090400	Strong transcription	Osteobl	bone
14	chr1:179072200-179090000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:179074200-179088200	Strong transcription	NHEK	skin
16	chr1:179074200-179091000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:179074400-179088200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:179074600-179083000	Strong transcription	Primary T cells from cord blood	blood
19	chr1:179075200-179091200	Strong transcription	NHLF	lung
20	chr1:179075400-179080000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:179075400-179084200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:179075400-179091000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:179075400-179091400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:179075400-179096200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:179075600-179080000	Strong transcription	Hela-S3	cervix
26	chr1:179075600-179080200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:179075600-179081000	Strong transcription	Fetal Brain Female	brain
28	chr1:179075600-179081800	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:179075600-179082000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:179075600-179082200	Strong transcription	Placenta	Placenta
31	chr1:179075600-179082800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr1:179075600-179084000	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:179075600-179089200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr1:179075800-179080000	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr1:179075800-179081000	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr1:179075800-179081600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:179075800-179082400	Strong transcription	Brain Angular Gyrus	brain
38	chr1:179075800-179082400	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr1:179075800-179082800	Strong transcription	Fetal Intestine Large	intestine
40	chr1:179075800-179082800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:179075800-179083600	Strong transcription	Lung	lung
42	chr1:179075800-179084600	Strong transcription	A549	lung
43	chr1:179075800-179089600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:179076000-179080000	Strong transcription	Brain Anterior Caudate	brain
45	chr1:179076000-179080000	Strong transcription	Rectal Smooth Muscle	rectum
46	chr1:179076000-179080800	Strong transcription	Brain Inferior Temporal Lobe	brain
47	chr1:179076000-179081600	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:179076000-179081600	Strong transcription	Primary B cells from peripheral blood	blood
49	chr1:179076000-179081600	Strong transcription	Ovary	ovary
50	chr1:179076000-179081800	Strong transcription	Fetal Thymus	thymus

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