Variant report

Variant	rs1009
Chromosome Location	chr2:85808737-85808738
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF384	chr2:85808425-85808813	K562	blood:	n/a	n/a
2	CTCF	chr2:85808640-85808790	K562	blood:	n/a	chr2:85808651-85808664
3	RCOR1	chr2:85808690-85808853	K562	blood:	n/a	n/a
4	CTCF	chr2:85808551-85808768	K562	blood:	n/a	chr2:85808651-85808664
5	CTCF	chr2:85808600-85808750	HRPEpiC	eye:	n/a	chr2:85808651-85808664

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:85787394..85789695-chr2:85806096..85808761,2	K562	blood:
2	chr2:85766314..85768748-chr2:85805954..85808781,2	MCF-7	breast:

Variant related genes	Relation type
VAMP5	TF binding region
ENSG00000168906	Chromatin interaction
ENSG00000115486	Chromatin interaction
ENSG00000118640	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs10179195	0.91[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10187424	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs10198569	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs10206961	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs1058588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs1078004	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1348818	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1446669	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1561198	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs17026396	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs2028898	0.86[CHB][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs2028900	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs2043675	0.86[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap]
rs2044474	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2166529	0.81[CHB][hapmap]
rs2289972	0.86[CHB][hapmap]
rs2592551	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs2886722	0.89[CEU][hapmap];0.81[CHB][hapmap];0.83[TSI][hapmap]
rs3731828	0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap]
rs3755015	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs3770098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6547621	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6705971	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap]
rs6738645	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6757263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs699664	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[JPT][hapmap]
rs7568458	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7579147	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs7591175	0.81[CHB][hapmap]
rs7593969	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs762684	0.86[CHB][hapmap];0.81[JPT][hapmap]

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1009	GGCX	cis	cerebellum	SCAN
rs1009	GGCX	cis	Whole Blood	GTEx
rs1009	VAMP8	cis	parietal	SCAN
rs1009	GGCX	cis	parietal	SCAN
rs1009	GGCX	cis	Artery Tibial	GTEx
rs1009	GGCX	cis	Thyroid	GTEx
rs1009	LOC388969	cis	multi-tissue	Pritchard
rs1009	VAMP8	cis	multi-tissue	Pritchard
rs1009	VAMP8	cis	Esophagus Mucosa	GTEx
rs1009	VAMP8	Cis_1M	lymphoblastoid	RTeQTL
rs1009	RNF103	cis	parietal	SCAN
rs1009	MAT2A	cis	cerebellum	SCAN
rs1009	VAMP8	cis	lymphoblastoid	seeQTL
rs1009	GGCX	cis	Artery Aorta	GTEx
rs1009	VAMP8	cis	uninvolved skin	skin_eQTL
rs1009	VAMP8	cis	lesional skin	skin_eQTL
rs1009	GGCX	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85805800-85810400	Weak transcription	Right Ventricle	heart
2	chr2:85805800-85810800	Weak transcription	Psoas Muscle	Psoas
3	chr2:85806200-85810800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr2:85806200-85811000	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:85806200-85811800	Weak transcription	A549	lung
6	chr2:85806400-85810800	Weak transcription	Left Ventricle	heart
7	chr2:85806800-85809000	Weak transcription	Hela-S3	cervix
8	chr2:85806800-85810400	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:85806800-85810600	Weak transcription	HUVEC	blood vessel
10	chr2:85806800-85811000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:85807000-85808800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:85807000-85810000	Genic enhancers	Placenta	Placenta
13	chr2:85807000-85810600	Weak transcription	Fetal Kidney	kidney
14	chr2:85807000-85810800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:85807000-85811000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:85807000-85811000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:85807000-85811400	Weak transcription	Small Intestine	intestine
18	chr2:85807200-85808800	Weak transcription	Colonic Mucosa	Colon
19	chr2:85807200-85810000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr2:85807200-85810400	Weak transcription	NHLF	lung
21	chr2:85807200-85810800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:85807200-85811000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:85807400-85809200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr2:85807400-85810000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:85807400-85810600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:85807400-85810800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:85807400-85810800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:85807400-85810800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:85807400-85810800	Weak transcription	HSMMtube	muscle
30	chr2:85807400-85811200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:85807600-85808800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:85807600-85808800	Weak transcription	Fetal Stomach	stomach
33	chr2:85807600-85809200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:85807600-85809400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:85807600-85809400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:85807600-85809400	Weak transcription	Brain Substantia Nigra	brain
37	chr2:85807600-85809600	Weak transcription	Adipose Nuclei	Adipose
38	chr2:85807600-85809600	Weak transcription	Brain Angular Gyrus	brain
39	chr2:85807600-85810000	Strong transcription	Primary B cells from peripheral blood	blood
40	chr2:85807600-85810400	Strong transcription	Primary T cells from cord blood	blood
41	chr2:85807600-85810400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:85807600-85810600	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr2:85807600-85810800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr2:85807600-85810800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr2:85807600-85810800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr2:85807600-85810800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:85807600-85810800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:85807600-85810800	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:85807600-85810800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:85807600-85810800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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