Variant report

Variant	rs1220
Chromosome Location	chr1:179045500-179045501
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:178993182..178999783-chr1:179045102..179052535,14	MCF-7	breast:
2	chr1:179035309..179037468-chr1:179043936..179046736,2	K562	blood:

Variant related genes	Relation type
ENSG00000116199	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10798649	1.00[ASW][hapmap];0.84[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10798650	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798651	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10913682	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2025584	0.81[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3753533	0.84[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3766626	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766628	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3820163	1.00[ASW][hapmap];0.80[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4297249	0.80[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4322196	0.80[ASN][1000 genomes]
rs6425513	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs7515519	0.90[AFR][1000 genomes]
rs7526438	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7549040	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs912758	0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9283394	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9725887	0.91[GIH][hapmap];0.93[TSI][hapmap]
rs9727621	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9727648	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1220	GPR52	cis	parietal	SCAN
rs1220	ABL2	cis	parietal	SCAN
rs1220	FAM20B	cis	multi-tissue	Pritchard
rs1220	FAM20B	cis	parietal	SCAN
rs1220	TOR3A	cis	Artery Tibial	GTEx
rs1220	FAM20B	cis	lymphoblastoid	seeQTL
rs1220	RALGPS2	cis	parietal	SCAN
rs1220	FAM20B	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179008600-179049800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:179008600-179049800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:179009600-179050400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:179025000-179050200	Weak transcription	HUVEC	blood vessel
5	chr1:179025400-179050600	Weak transcription	Fetal Brain Male	brain
6	chr1:179025600-179050000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:179025600-179050400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:179025800-179050200	Weak transcription	Fetal Heart	heart
9	chr1:179027800-179050600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:179028600-179050000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:179028600-179050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:179033800-179050000	Weak transcription	Esophagus	oesophagus
13	chr1:179034000-179050000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:179034200-179050000	Weak transcription	Colonic Mucosa	Colon
15	chr1:179034200-179050000	Weak transcription	Fetal Kidney	kidney
16	chr1:179035400-179050000	Weak transcription	Fetal Lung	lung
17	chr1:179036000-179046800	Weak transcription	NHLF	lung
18	chr1:179036200-179046400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:179036200-179049200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:179036200-179050200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:179036200-179050800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr1:179036400-179049200	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:179036400-179050000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:179036400-179050200	Weak transcription	Stomach Mucosa	stomach
25	chr1:179036400-179050400	Weak transcription	Right Ventricle	heart
26	chr1:179038400-179049800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:179038400-179049800	Weak transcription	HepG2	liver
28	chr1:179038600-179050000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:179040600-179046200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:179041000-179046400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:179041600-179046200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:179041600-179050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:179041600-179050000	Weak transcription	Colon Smooth Muscle	Colon
34	chr1:179041600-179050000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:179041600-179050000	Weak transcription	NHEK	skin
36	chr1:179041600-179050200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:179041600-179050200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:179041600-179050200	Weak transcription	Brain Substantia Nigra	brain
39	chr1:179041600-179050200	Weak transcription	Fetal Stomach	stomach
40	chr1:179041600-179050600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:179041600-179050600	Weak transcription	Lung	lung
42	chr1:179041800-179048200	Weak transcription	Liver	Liver
43	chr1:179041800-179049600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr1:179041800-179049800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:179041800-179049800	Weak transcription	Pancreas	Pancrea
46	chr1:179041800-179049800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:179041800-179050200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr1:179041800-179050200	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr1:179041800-179050200	Weak transcription	Spleen	Spleen
50	chr1:179041800-179050400	Weak transcription	Small Intestine	intestine

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