Variant report

Variant	rs1046385
Chromosome Location	chr1:179064875-179064876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10082052	0.81[CEU][hapmap]
rs10458367	0.81[AMR][1000 genomes]
rs10798652	0.81[JPT][hapmap]
rs10913691	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1173077	0.85[JPT][hapmap]
rs12408349	1.00[ASW][hapmap]
rs1325194	1.00[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17362081	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2050922	0.83[ASN][1000 genomes]
rs2066162	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2296377	0.87[GIH][hapmap];0.85[AMR][1000 genomes]
rs2636266	1.00[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap]
rs2636278	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs2636287	0.89[JPT][hapmap]
rs2636290	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793791	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2793799	0.85[JPT][hapmap]
rs2793805	1.00[ASW][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs2816209	0.85[JPT][hapmap]
rs3210839	0.85[JPT][hapmap];0.81[TSI][hapmap]
rs3813638	1.00[ASW][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap]
rs3818433	1.00[ASW][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4651014	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4652348	0.80[CEU][hapmap]
rs6425512	1.00[ASW][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs7544801	1.00[ASW][hapmap];0.80[CEU][hapmap];0.90[GIH][hapmap];0.80[TSI][hapmap]
rs912758	0.81[CEU][hapmap]
rs931441	0.94[CHB][hapmap];1.00[JPT][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1046385	LHX4	cis	parietal	SCAN
rs1046385	ABL2	cis	parietal	SCAN
rs1046385	FAM20B	cis	parietal	SCAN
rs1046385	FAM20B	cis	cerebellum	SCAN
rs1046385	RALGPS2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179053000-179072200	Strong transcription	Primary T cells from cord blood	blood
2	chr1:179053200-179067600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:179053200-179071000	Strong transcription	NHEK	skin
4	chr1:179053200-179096000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:179053400-179067400	Strong transcription	Fetal Intestine Small	intestine
6	chr1:179053800-179066600	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:179053800-179066800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:179053800-179067200	Strong transcription	Thymus	Thymus
9	chr1:179053800-179069000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:179053800-179074600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:179054000-179067600	Strong transcription	Fetal Intestine Large	intestine
12	chr1:179054000-179071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:179054000-179074800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:179054000-179077200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:179054000-179079400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:179054400-179067200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:179054400-179067800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr1:179054600-179066600	Strong transcription	Fetal Brain Female	brain
19	chr1:179054600-179067200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr1:179054800-179065600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:179054800-179066800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:179054800-179067200	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:179054800-179067600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:179054800-179067800	Strong transcription	Brain Germinal Matrix	brain
25	chr1:179054800-179072200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:179055800-179066400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:179056000-179065800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:179056200-179066400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:179056200-179066600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr1:179056400-179067400	Strong transcription	Fetal Thymus	thymus
31	chr1:179056600-179066600	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr1:179056600-179067800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:179056600-179068000	Strong transcription	Dnd41	blood
34	chr1:179057000-179067800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:179057200-179076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:179057400-179068800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:179057600-179067200	Strong transcription	HMEC	breast
38	chr1:179058000-179067400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr1:179059000-179066800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:179059000-179066800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:179059200-179066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:179059200-179096400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:179059400-179067000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr1:179059400-179067800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:179059400-179090400	Strong transcription	HUVEC	blood vessel
46	chr1:179059600-179066800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr1:179059600-179067400	Strong transcription	K562	blood
48	chr1:179059600-179067800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:179059600-179067800	Strong transcription	Brain Hippocampus Middle	brain
50	chr1:179059800-179068000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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