Variant report

Variant	rs3856467
Chromosome Location	chr2:10917594-10917595
allele	A/G
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	POLR2A	chr2:10917361-10917743	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:10917017-10917772	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr2:10916599-10917854	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:10916307-10919284	K562	blood:	n/a	n/a
5	POLR2A	chr2:10917419-10918091	K562	blood:	n/a	n/a
6	POLR2A	chr2:10915153-10919303	K562	blood:	n/a	n/a
7	FOSL2	chr2:10916758-10917688	HepG2	liver:	n/a	n/a
8	POLR2A	chr2:10916350-10919110	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr2:10917147-10917927	MCF-7	breast:	n/a	n/a
10	POLR2A	chr2:10916527-10918208	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr2:10917230-10918019	K562	blood:	n/a	n/a
12	POLR2A	chr2:10917446-10917681	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10897264..10897998-chr2:10917360..10918173,2	MCF-7	breast:

Variant related genes	Relation type
ATP6V1C2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10182400	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192112	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10197595	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10200007	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10520049	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11489	0.94[EUR][1000 genomes]
rs11885932	0.83[EUR][1000 genomes]
rs12617247	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617440	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13404780	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1387568	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17364770	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs17364812	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17365015	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs17365299	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455729	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17455876	0.86[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs2357816	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714903	0.94[EUR][1000 genomes]
rs6718547	0.94[EUR][1000 genomes]
rs6722515	0.95[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs6733037	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756520	0.92[EUR][1000 genomes]
rs73174526	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7561135	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570179	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000953	chr2:10717304-10921805	Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv535584	chr2:10717304-10921805	Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1000731	chr2:10758657-10943882	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3856467	PDIA6	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10905600-10918000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:10906200-10918200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr2:10906200-10918400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:10908000-10918200	Weak transcription	Pancreas	Pancrea
5	chr2:10908000-10918400	Weak transcription	Aorta	Aorta
6	chr2:10908600-10924400	Weak transcription	Psoas Muscle	Psoas
7	chr2:10908800-10918200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:10911400-10917600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:10912200-10918200	Weak transcription	Primary B cells from cord blood	blood
10	chr2:10912800-10917600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr2:10913200-10917800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr2:10913200-10918200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:10913200-10920200	Weak transcription	NH-A	brain
14	chr2:10913400-10920200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:10913600-10918400	Weak transcription	HSMM	muscle
16	chr2:10913600-10919800	Weak transcription	Osteobl	bone
17	chr2:10914200-10920000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:10914400-10918000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:10914600-10918400	Weak transcription	HepG2	liver
20	chr2:10914600-10920200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:10914600-10922400	Weak transcription	Fetal Kidney	kidney
22	chr2:10914600-10931600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:10914800-10918600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:10915000-10917800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:10915000-10918200	Weak transcription	A549	lung
26	chr2:10915000-10920000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:10915000-10920000	Weak transcription	Brain Angular Gyrus	brain
28	chr2:10915000-10921600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:10915200-10917600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:10915200-10918000	Weak transcription	Colonic Mucosa	Colon
31	chr2:10915200-10920200	Weak transcription	HSMMtube	muscle
32	chr2:10915200-10923000	Weak transcription	Fetal Brain Male	brain
33	chr2:10915400-10917600	Weak transcription	Brain Germinal Matrix	brain
34	chr2:10915400-10918000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:10915600-10917600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:10915600-10917800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:10915600-10918000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:10915600-10918000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:10915600-10918400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr2:10915600-10918600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:10915600-10920000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:10915600-10920200	Weak transcription	HMEC	breast
43	chr2:10915600-10920400	Weak transcription	Stomach Mucosa	stomach
44	chr2:10915600-10921800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:10915600-10939800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:10915600-10950400	Weak transcription	Right Atrium	heart
47	chr2:10915800-10917800	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:10915800-10918000	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr2:10915800-10918600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:10915800-10920000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links