Variant report

Variant	rs340163
Chromosome Location	chr3:111834753-111834754
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111833855..111836501-chr3:111839924..111841508,2	MCF-7	breast:
2	chr3:111832694..111835578-chr3:112096846..112099201,2	MCF-7	breast:
3	chr3:111833809..111835627-chr3:111838661..111841118,2	K562	blood:
4	chr3:111829764..111831902-chr3:111832844..111835474,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114529	Chromatin interaction
ENSG00000207940	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1032398	0.81[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs10934145	0.83[CHB][hapmap]
rs10934162	0.81[CHB][hapmap]
rs11707558	0.83[CHB][hapmap]
rs11824	0.89[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs11922559	0.83[CHB][hapmap]
rs12172949	0.89[JPT][hapmap]
rs12172961	0.89[JPT][hapmap]
rs12488760	0.83[CHB][hapmap]
rs12634769	0.83[CHB][hapmap]
rs13063452	0.82[CEU][hapmap]
rs13074229	0.81[CEU][hapmap]
rs13081485	0.89[CHB][hapmap]
rs13081935	0.83[CHB][hapmap]
rs13082509	0.83[CHB][hapmap]
rs13087086	0.83[CHB][hapmap]
rs13091454	0.90[CHB][hapmap]
rs13100724	0.83[CHB][hapmap]
rs1388858	0.80[CEU][hapmap]
rs16859207	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17446744	0.82[ASW][hapmap];0.84[CEU][hapmap];0.83[CHB][hapmap]
rs2120095	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs340164	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs340165	0.89[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs340172	0.85[CEU][hapmap]
rs3856723	0.89[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs4234412	0.83[CHB][hapmap]
rs4234413	0.91[CHB][hapmap]
rs4276157	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4282033	0.83[CHB][hapmap]
rs4300982	0.83[CHB][hapmap]
rs4392388	0.83[CHB][hapmap]
rs4398404	0.81[CHB][hapmap]
rs4401342	0.83[CHB][hapmap]
rs4505669	0.83[CHB][hapmap]
rs4560270	0.83[CHB][hapmap]
rs4572740	0.83[CHB][hapmap]
rs4585166	0.83[CHB][hapmap]
rs4611789	0.83[CHB][hapmap]
rs4632517	0.83[CHB][hapmap]
rs4682097	0.83[CHB][hapmap]
rs4682357	0.85[CEU][hapmap]
rs4682367	0.86[CEU][hapmap]
rs4682380	0.83[CHB][hapmap]
rs58167335	0.87[ASN][1000 genomes]
rs6773916	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs6781344	0.83[CHB][hapmap]
rs6798551	0.83[CHB][hapmap]
rs729641	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs7613061	0.83[CHB][hapmap]
rs7616261	0.83[CHB][hapmap]
rs7624367	0.83[CHB][hapmap]
rs7627314	0.84[CEU][hapmap];0.83[CHB][hapmap]
rs7638520	0.83[CHB][hapmap]
rs923745	0.86[EUR][1000 genomes]
rs9758396	0.83[CHB][hapmap]
rs9809384	0.83[CHB][hapmap]
rs9809404	0.83[CHB][hapmap]
rs9822786	0.83[CHB][hapmap]
rs9823421	0.83[CHB][hapmap]
rs9826043	0.82[CHB][hapmap]
rs9847574	0.82[CHB][hapmap]
rs9860819	0.83[CHB][hapmap]
rs9863061	0.82[CHB][hapmap]
rs9878213	0.83[CHB][hapmap]
rs9879184	0.82[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs340163	GCET2	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111810400-111852000	Weak transcription	Esophagus	oesophagus
2	chr3:111812000-111844000	Weak transcription	Colonic Mucosa	Colon
3	chr3:111812000-111845600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
5	chr3:111812400-111835800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:111812600-111840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:111814400-111836000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:111819000-111840400	Weak transcription	Fetal Stomach	stomach
9	chr3:111819600-111847800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:111821000-111835800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:111821200-111843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:111821400-111839000	Weak transcription	Osteobl	bone
13	chr3:111821400-111843600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:111821600-111834800	Weak transcription	HUVEC	blood vessel
15	chr3:111822000-111844600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:111822400-111839200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:111822800-111835600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:111823400-111837800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:111825600-111838600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:111825800-111835400	Weak transcription	Aorta	Aorta
21	chr3:111825800-111835600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:111825800-111844400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:111827000-111838600	Weak transcription	Spleen	Spleen
24	chr3:111828200-111838600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:111828400-111838200	Weak transcription	Stomach Mucosa	stomach
26	chr3:111828600-111835600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr3:111828800-111835600	Weak transcription	Left Ventricle	heart
28	chr3:111829600-111836400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:111830000-111835600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:111830000-111837800	Strong transcription	NHEK	skin
31	chr3:111830600-111835600	Enhancers	Thymus	Thymus
32	chr3:111830600-111853200	Weak transcription	Lung	lung
33	chr3:111830800-111845400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:111831000-111835800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:111831200-111837400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:111831200-111838800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:111831400-111836200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr3:111831400-111843000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:111832000-111844600	Weak transcription	Hela-S3	cervix
40	chr3:111832400-111835400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:111832400-111838600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr3:111832400-111840600	Enhancers	Primary B cells from cord blood	blood
43	chr3:111832600-111835600	Weak transcription	Fetal Intestine Large	intestine
44	chr3:111832600-111841600	Enhancers	Primary B cells from peripheral blood	blood
45	chr3:111832800-111836200	Enhancers	Fetal Muscle Leg	muscle
46	chr3:111833000-111838600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:111833200-111835200	Weak transcription	NH-A	brain
48	chr3:111833200-111835400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:111833200-111835600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr3:111833200-111837600	Weak transcription	HMEC	breast

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