Variant report

Variant	rs1894633
Chromosome Location	chr1:172331059-172331060
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:172221315..172226024-chr1:172325981..172331432,5	MCF-7	breast:
2	chr1:172224104..172227089-chr1:172327866..172331463,5	MCF-7	breast:
3	chr1:172330690..172333183-chr1:172340261..172343230,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1011731	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs1023479	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs10489284	0.89[CHB][hapmap]
rs10752943	0.81[ASN][1000 genomes]
rs10752944	0.89[CHB][hapmap]
rs10797996	0.82[ASN][1000 genomes]
rs10911654	0.82[ASN][1000 genomes]
rs10911684	0.89[CHB][hapmap]
rs12404665	0.82[ASN][1000 genomes]
rs2001129	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs2032528	0.88[CHB][hapmap]
rs2213731	0.89[CHB][hapmap]
rs2213732	0.82[ASN][1000 genomes]
rs2227198	0.89[CHB][hapmap]
rs2227199	0.89[CHB][hapmap]
rs2227200	0.84[ASN][1000 genomes]
rs2269612	0.82[ASN][1000 genomes]
rs2301453	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs3213564	0.83[ASW][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs3768445	0.89[CHB][hapmap]
rs4471302	0.89[CHB][hapmap]
rs4504922	0.80[ASN][1000 genomes]
rs4916251	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs4916252	0.82[ASN][1000 genomes]
rs57668887	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6424894	0.89[CHB][hapmap]
rs6676665	0.89[CHB][hapmap]
rs6697844	0.95[ASN][1000 genomes]
rs6698987	0.89[CHB][hapmap]
rs714515	0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs73046851	0.98[ASN][1000 genomes]
rs7534393	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9286854	0.89[CHB][hapmap]
rs9425291	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9425301	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs9425568	0.95[ASN][1000 genomes]
rs9425573	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425575	0.98[ASN][1000 genomes]
rs9425579	0.80[ASN][1000 genomes]
rs9425586	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs9425587	0.82[ASN][1000 genomes]
rs9425589	0.82[ASN][1000 genomes]
rs9425592	0.89[CHB][hapmap]
rs9425628	0.88[CHB][hapmap]
rs979935	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv3543	chr1:172323563-172334586	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1894633	PIGC	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172320800-172332800	Enhancers	Fetal Intestine Small	intestine
2	chr1:172323000-172333000	Enhancers	Fetal Intestine Large	intestine
3	chr1:172325800-172331400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:172326400-172331200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:172326600-172332200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr1:172327000-172331200	Enhancers	Primary B cells from peripheral blood	blood
7	chr1:172327000-172331200	Enhancers	Fetal Stomach	stomach
8	chr1:172327200-172332200	Enhancers	Brain Substantia Nigra	brain
9	chr1:172328000-172332400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr1:172328200-172331200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:172328400-172331200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:172328400-172331400	Enhancers	Fetal Lung	lung
13	chr1:172328400-172331600	Weak transcription	Brain Germinal Matrix	brain
14	chr1:172328400-172334000	Weak transcription	Aorta	Aorta
15	chr1:172329000-172332000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr1:172329000-172332400	Weak transcription	Fetal Brain Male	brain
17	chr1:172329200-172331200	Enhancers	Fetal Kidney	kidney
18	chr1:172329200-172334600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:172329600-172331200	Enhancers	Spleen	Spleen
20	chr1:172329800-172334000	Weak transcription	Left Ventricle	heart
21	chr1:172329800-172334000	Weak transcription	Osteobl	bone
22	chr1:172330000-172331200	Flanking Active TSS	GM12878-XiMat	blood
23	chr1:172330200-172331200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr1:172330200-172332200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr1:172330400-172331600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:172330400-172331800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:172330400-172332000	Weak transcription	A549	lung
28	chr1:172330400-172332200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr1:172330400-172332200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:172330400-172336600	Weak transcription	Colon Smooth Muscle	Colon
31	chr1:172330400-172343000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:172330600-172331400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr1:172330600-172332200	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr1:172330800-172332000	Weak transcription	Brain Anterior Caudate	brain
35	chr1:172331000-172331200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
36	chr1:172331000-172331200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:172331000-172331600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
38	chr1:172331000-172331800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr1:172331000-172332000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:172331000-172332000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:172331000-172332000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:172331000-172336400	Weak transcription	Small Intestine	intestine

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