Variant report

Variant	rs10798652
Chromosome Location	chr1:179061427-179061428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179059594..179062253-chr1:179196494..179198412,2	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1046385	0.81[JPT][hapmap]
rs1173077	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs12130276	0.82[JPT][hapmap]
rs1856968	0.81[JPT][hapmap]
rs2636287	0.95[JPT][hapmap]
rs2793799	0.95[JPT][hapmap]
rs2816209	0.95[JPT][hapmap];0.83[MEX][hapmap]
rs3210839	0.95[JPT][hapmap];0.87[MEX][hapmap]
rs3818433	0.81[JPT][hapmap]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10798652	FAM20B	cis	cerebellum	SCAN
rs10798652	TOR3A	cis	Artery Tibial	GTEx
rs10798652	FAM20B	cis	parietal	SCAN
rs10798652	FAM20B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179052200-179062200	Weak transcription	Small Intestine	intestine
2	chr1:179052400-179062600	Weak transcription	Fetal Kidney	kidney
3	chr1:179052600-179064200	Weak transcription	Fetal Brain Male	brain
4	chr1:179053000-179072200	Strong transcription	Primary T cells from cord blood	blood
5	chr1:179053200-179062400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:179053200-179063000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:179053200-179064000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr1:179053200-179067600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:179053200-179071000	Strong transcription	NHEK	skin
10	chr1:179053200-179096000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:179053400-179062000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:179053400-179062200	Weak transcription	Stomach Mucosa	stomach
13	chr1:179053400-179067400	Strong transcription	Fetal Intestine Small	intestine
14	chr1:179053800-179066600	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr1:179053800-179066800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr1:179053800-179067200	Strong transcription	Thymus	Thymus
17	chr1:179053800-179069000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:179053800-179074600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:179054000-179067600	Strong transcription	Fetal Intestine Large	intestine
20	chr1:179054000-179071000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:179054000-179074800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:179054000-179077200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:179054000-179079400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:179054400-179067200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:179054400-179067800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:179054600-179066600	Strong transcription	Fetal Brain Female	brain
27	chr1:179054600-179067200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr1:179054800-179065600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:179054800-179066800	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:179054800-179067200	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:179054800-179067600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:179054800-179067800	Strong transcription	Brain Germinal Matrix	brain
33	chr1:179054800-179072200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:179055800-179066400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:179056000-179065800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:179056200-179066400	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr1:179056200-179066600	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:179056400-179062200	Weak transcription	Brain Substantia Nigra	brain
39	chr1:179056400-179067400	Strong transcription	Fetal Thymus	thymus
40	chr1:179056600-179066600	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr1:179056600-179067800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr1:179056600-179068000	Strong transcription	Dnd41	blood
43	chr1:179057000-179067800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:179057200-179076800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:179057400-179068800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:179057600-179067200	Strong transcription	HMEC	breast
47	chr1:179058000-179062200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr1:179058000-179067400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:179058200-179063200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr1:179058600-179061600	Genic enhancers	Placenta	Placenta

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