Variant report

Variant	rs773658
Chromosome Location	chr12:56603834-56603835
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56600189..56603854-chr12:56613542..56616774,5	MCF-7	breast:
2	chr12:56601536..56604382-chr12:56651037..56652790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139645	Chromatin interaction
ENSG00000181852	Chromatin interaction
ENSG00000139579	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10129008	1.00[EUR][1000 genomes]
rs10747763	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10876878	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171753	1.00[TSI][hapmap]
rs11171754	1.00[EUR][1000 genomes]
rs11171755	1.00[EUR][1000 genomes]
rs11171772	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11171777	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11171823	1.00[TSI][hapmap]
rs11834728	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229022	0.95[ASN][1000 genomes]
rs12306670	1.00[TSI][hapmap]
rs12309480	1.00[EUR][1000 genomes]
rs12311878	1.00[TSI][hapmap]
rs12320265	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274502	1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405859	1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1689518	1.00[CHD][hapmap]
rs17118333	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2271188	1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs2271190	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2271192	1.00[JPT][hapmap]
rs2277340	1.00[CHD][hapmap]
rs2463365	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629451	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2629453	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2695783	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695784	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28676339	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2930787	0.89[AMR][1000 genomes]
rs2930788	0.94[ASW][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950573	1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759096	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3802996	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3809130	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4759218	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55887836	1.00[EUR][1000 genomes]
rs56851901	0.83[ASN][1000 genomes]
rs57280585	0.83[ASN][1000 genomes]
rs57822276	0.83[ASN][1000 genomes]
rs58009483	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58476735	0.83[ASN][1000 genomes]
rs58548156	0.83[ASN][1000 genomes]
rs58663297	0.83[ASN][1000 genomes]
rs59053322	1.00[ASN][1000 genomes]
rs59078852	1.00[ASN][1000 genomes]
rs59420211	1.00[EUR][1000 genomes]
rs59966703	1.00[ASN][1000 genomes]
rs60396934	0.83[ASN][1000 genomes]
rs61939011	1.00[ASN][1000 genomes]
rs6581091	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs703823	0.94[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136420	1.00[TSI][hapmap]
rs7311008	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73340401	1.00[EUR][1000 genomes]
rs74092003	1.00[EUR][1000 genomes]
rs7489249	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772925	1.00[TSI][hapmap]
rs772926	1.00[TSI][hapmap]
rs773654	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773655	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs773659	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773660	0.90[ASN][1000 genomes]
rs773661	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773663	1.00[TSI][hapmap]
rs7956599	0.90[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7956926	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7962107	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7967464	1.00[ASN][1000 genomes]
rs7975405	1.00[ASN][1000 genomes]
rs7975486	1.00[TSI][hapmap]

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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs773658	MYL6B	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56585000-56614800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56592600-56613600	Weak transcription	Right Atrium	heart
3	chr12:56596600-56604000	Weak transcription	Small Intestine	intestine
4	chr12:56597800-56610600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr12:56597800-56610600	Strong transcription	Fetal Lung	lung
6	chr12:56597800-56611600	Strong transcription	Primary T cells from cord blood	blood
7	chr12:56597800-56611600	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr12:56597800-56611800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr12:56597800-56611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:56597800-56611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr12:56597800-56611800	Strong transcription	Fetal Muscle Leg	muscle
12	chr12:56597800-56611800	Strong transcription	Fetal Thymus	thymus
13	chr12:56597800-56612000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:56598000-56606400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr12:56598000-56610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:56598000-56610600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr12:56598000-56610600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr12:56598000-56610600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:56598000-56610600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:56598000-56610600	Strong transcription	Brain Hippocampus Middle	brain
21	chr12:56598000-56610600	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr12:56598000-56610600	Strong transcription	Spleen	Spleen
23	chr12:56598000-56611000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:56598000-56611000	Strong transcription	Stomach Smooth Muscle	stomach
25	chr12:56598000-56611600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:56598000-56611600	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr12:56598000-56611600	Strong transcription	Fetal Brain Female	brain
28	chr12:56598000-56611600	Strong transcription	Fetal Intestine Large	intestine
29	chr12:56598000-56611600	Strong transcription	Fetal Muscle Trunk	muscle
30	chr12:56598000-56611800	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr12:56598000-56613600	Strong transcription	Fetal Stomach	stomach
32	chr12:56598200-56609000	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr12:56598200-56609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr12:56598200-56610400	Strong transcription	Duodenum Smooth Muscle	Duodenum
35	chr12:56598200-56610600	Strong transcription	H1 Cell Line	embryonic stem cell
36	chr12:56598200-56610600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr12:56598200-56610600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:56598200-56610600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:56598200-56610600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr12:56598200-56611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:56598200-56611800	Strong transcription	Placenta	Placenta
42	chr12:56598200-56611800	Strong transcription	Thymus	Thymus
43	chr12:56598200-56613800	Strong transcription	Fetal Intestine Small	intestine
44	chr12:56598400-56604000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:56598400-56610600	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr12:56598400-56610600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:56598400-56610600	Strong transcription	HSMMtube	muscle
48	chr12:56598400-56610800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:56598400-56611400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:56598400-56611800	Strong transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links