Variant report

Variant	rs1146637
Chromosome Location	chr1:76256618-76256619
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:43)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:43 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:76249993-76263987	K562	blood:	n/a	n/a
2	POLR2A	chr1:76256156-76256996	K562	blood:	n/a	n/a
3	POLR2A	chr1:76255728-76256819	K562	blood:	n/a	n/a
4	POLR2A	chr1:76256191-76256857	K562	blood:	n/a	n/a
5	POLR2A	chr1:76250010-76263479	K562	blood:	n/a	n/a
6	POLR2A	chr1:76250991-76264029	PFSK-1	brain:	n/a	n/a
7	CEBPB	chr1:76256319-76257252	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:76250033-76264125	K562	blood:	n/a	n/a
9	POLR2A	chr1:76256556-76258577	U87	brain:	n/a	n/a
10	POLR2A	chr1:76251073-76257428	HepG2	liver:	n/a	n/a
11	GATA3	chr1:76256554-76257398	MCF-7	breast:	n/a	n/a
12	HEY1	chr1:76256235-76256687	K562	blood:	n/a	n/a
13	POLR2A	chr1:76256349-76257207	K562	blood:	n/a	n/a
14	POLR2A	chr1:76251198-76257365	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr1:76251042-76257307	U87	brain:	n/a	n/a
16	HEY1	chr1:76256558-76257725	HepG2	liver:	n/a	n/a
17	POLR2A	chr1:76250068-76266595	GM12878	blood:	n/a	n/a
18	POLR2A	chr1:76251108-76257452	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr1:76256596-76258577	U87	brain:	n/a	n/a
20	POLR2A	chr1:76256200-76256663	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:76256223-76256972	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:76256226-76257332	K562	blood:	n/a	n/a
23	POLR2A	chr1:76250047-76263901	GM18505	blood:	n/a	n/a
24	POLR2A	chr1:76249945-76266639	GM12891	blood:	n/a	n/a
25	POLR2A	chr1:76256279-76256636	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:76256268-76256940	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr1:76256198-76256790	HCT-116	colon:	n/a	n/a
28	POLR2A	chr1:76256289-76257430	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr1:76250036-76264085	K562	blood:	n/a	n/a
30	POLR2A	chr1:76256509-76257010	MCF10A-Er-Src	breast:	n/a	n/a
31	SIN3AK20	chr1:76256582-76257337	MCF-7	breast:	n/a	n/a
32	POLR2A	chr1:76256356-76257312	PANC-1	pancreas:	n/a	n/a
33	POLR2A	chr1:76250200-76257400	GM19099	blood:	n/a	n/a
34	POLR2A	chr1:76255628-76257400	HepG2	liver:	n/a	n/a
35	POLR2A	chr1:76255510-76257063	SK-N-MC	brain:	n/a	n/a
36	POLR2A	chr1:76250996-76257615	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr1:76251203-76256991	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr1:76250185-76257476	GM12892	blood:	n/a	n/a
39	POLR2A	chr1:76255688-76257449	HUVEC	blood vessel:	n/a	n/a
40	POLR2A	chr1:76250012-76264059	K562	blood:	n/a	n/a
41	POLR2A	chr1:76256064-76257003	HepG2	liver:	n/a	n/a
42	POLR2A	chr1:76251020-76258361	U87	brain:	n/a	n/a
43	POLR2A	chr1:76256247-76256927	GM12892	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:76186306..76195796-chr1:76248732..76266552,73	K562	blood:
2	chr1:76187424..76195796-chr1:76248839..76258922,52	K562	blood:
3	chr1:76213598..76215985-chr1:76254500..76257122,2	K562	blood:

No data

Variant related genes	Relation type
RABGGTB	TF binding region
ENSG00000178193	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10873729	0.83[EUR][1000 genomes]
rs10873733	0.81[EUR][1000 genomes]
rs11161598	0.80[EUR][1000 genomes]
rs11161688	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161718	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1144340	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146607	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146609	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146610	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1146617	0.81[EUR][1000 genomes]
rs1146630	0.80[AMR][1000 genomes]
rs1146631	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1146632	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1146634	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146635	0.81[EUR][1000 genomes]
rs1146636	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146639	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1146642	0.81[AMR][1000 genomes]
rs1146643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1146644	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12092388	0.80[EUR][1000 genomes]
rs12734931	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5745323	0.91[EUR][1000 genomes];0.89[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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1146637	MSH4	cis	Artery Tibial	GTEx
rs1146637	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs1146637	MSH4	cis	Muscle Skeletal	GTEx
rs1146637	MSH4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76252200-76258400	Weak transcription	Spleen	Spleen
2	chr1:76252400-76258800	Transcr. at gene 5' and 3'	K562	blood
3	chr1:76252600-76257600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:76252800-76256800	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr1:76252800-76257000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
6	chr1:76252800-76257000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
7	chr1:76252800-76257200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
8	chr1:76253000-76256800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
9	chr1:76253000-76257400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
10	chr1:76253200-76257400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:76253400-76256800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:76253600-76256800	Genic enhancers	Primary monocytes fromperipheralblood	blood
13	chr1:76253600-76257400	Transcr. at gene 5' and 3'	Hela-S3	cervix
14	chr1:76253800-76257000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
15	chr1:76254000-76257000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:76254000-76260000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:76254200-76257400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:76254200-76258400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:76254200-76258600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
20	chr1:76254200-76263200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:76254400-76256800	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
22	chr1:76254400-76257400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr1:76254400-76262400	Strong transcription	Placenta	Placenta
24	chr1:76254400-76265200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr1:76254600-76256800	Transcr. at gene 5' and 3'	NHEK	skin
26	chr1:76254600-76257000	Transcr. at gene 5' and 3'	A549	lung
27	chr1:76254600-76257600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr1:76254800-76256800	Genic enhancers	Fetal Intestine Large	intestine
29	chr1:76254800-76258200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr1:76254800-76258400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:76254800-76262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:76254800-76262600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr1:76255000-76256800	Genic enhancers	Primary T cells fromperipheralblood	blood
34	chr1:76255000-76257000	Transcr. at gene 5' and 3'	HepG2	liver
35	chr1:76255000-76257200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
36	chr1:76255000-76257400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:76255200-76256800	Genic enhancers	Rectal Mucosa Donor 31	rectum
38	chr1:76255200-76257000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr1:76255200-76257000	Genic enhancers	Osteobl	bone
40	chr1:76255200-76257400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr1:76255200-76261400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:76255200-76263600	Strong transcription	Fetal Lung	lung
43	chr1:76255400-76256800	Genic enhancers	Monocytes-CD14+_RO01746	blood
44	chr1:76255400-76256800	Genic enhancers	NHDF-Ad	bronchial
45	chr1:76255400-76257400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:76255400-76257400	Genic enhancers	HSMM	muscle
47	chr1:76255400-76262600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
48	chr1:76255400-76263000	Strong transcription	H1 Cell Line	embryonic stem cell
49	chr1:76255400-76265200	Weak transcription	Right Atrium	heart
50	chr1:76255600-76256800	Genic enhancers	Colonic Mucosa	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links