Variant report

Variant	rs773661
Chromosome Location	chr12:56602896-56602897
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56600189..56603854-chr12:56613542..56616774,5	MCF-7	breast:
2	chr12:56598444..56603105-chr12:56614822..56617186,4	K562	blood:
3	chr12:56596803..56602914-chr12:56614556..56619492,8	MCF-7	breast:
4	chr12:56601536..56604382-chr12:56651037..56652790,2	MCF-7	breast:
5	chr12:56598742..56603625-chr12:56603929..56607820,7	K562	blood:

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

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10129008	1.00[EUR][1000 genomes]
rs10747763	0.95[ASN][1000 genomes]
rs10876878	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11171754	1.00[EUR][1000 genomes]
rs11171755	1.00[EUR][1000 genomes]
rs11171772	1.00[ASN][1000 genomes]
rs11171777	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11834728	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12229022	0.95[ASN][1000 genomes]
rs12309480	1.00[EUR][1000 genomes]
rs12320265	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274502	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274503	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1405859	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118333	0.83[ASN][1000 genomes]
rs2271188	0.83[ASN][1000 genomes]
rs2271190	0.83[ASN][1000 genomes]
rs2463365	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629451	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2629453	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2695783	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695784	0.83[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	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2950573	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759096	0.83[ASN][1000 genomes]
rs3802996	0.83[ASN][1000 genomes]
rs3809130	0.83[ASN][1000 genomes]
rs4759218	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	0.95[ASN][1000 genomes]
rs703823	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311008	0.95[ASN][1000 genomes]
rs73340401	1.00[EUR][1000 genomes]
rs74092003	1.00[EUR][1000 genomes]
rs7489249	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773654	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs773655	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs773658	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773659	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773660	0.90[ASN][1000 genomes]
rs7956599	0.92[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7956926	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7962107	1.00[ASN][1000 genomes]
rs7967464	1.00[ASN][1000 genomes]
rs7975405	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
4	nsv973989	chr12:56582243-56602996	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

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	chr12:56596400-56603800	Weak transcription	Stomach Mucosa	stomach
4	chr12:56596600-56604000	Weak transcription	Small Intestine	intestine
5	chr12:56597800-56610600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:56597800-56610600	Strong transcription	Fetal Lung	lung
7	chr12:56597800-56611600	Strong transcription	Primary T cells from cord blood	blood
8	chr12:56597800-56611600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:56597800-56611800	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:56597800-56611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:56597800-56611800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:56597800-56611800	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:56597800-56611800	Strong transcription	Fetal Thymus	thymus
14	chr12:56597800-56612000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr12:56598000-56606400	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:56598000-56610400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:56598000-56610600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr12:56598000-56610600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:56598000-56610600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr12:56598000-56610600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr12:56598000-56610600	Strong transcription	Brain Hippocampus Middle	brain
22	chr12:56598000-56610600	Strong transcription	Rectal Mucosa Donor 31	rectum
23	chr12:56598000-56610600	Strong transcription	Spleen	Spleen
24	chr12:56598000-56611000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:56598000-56611000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr12:56598000-56611600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr12:56598000-56611600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:56598000-56611600	Strong transcription	Fetal Brain Female	brain
29	chr12:56598000-56611600	Strong transcription	Fetal Intestine Large	intestine
30	chr12:56598000-56611600	Strong transcription	Fetal Muscle Trunk	muscle
31	chr12:56598000-56611800	Strong transcription	H9 Cell Line	embryonic stem cell
32	chr12:56598000-56613600	Strong transcription	Fetal Stomach	stomach
33	chr12:56598200-56603800	Strong transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:56598200-56609000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:56598200-56609800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:56598200-56610400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:56598200-56610600	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr12:56598200-56610600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:56598200-56610600	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:56598200-56610600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:56598200-56610600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr12:56598200-56611800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:56598200-56611800	Strong transcription	Placenta	Placenta
44	chr12:56598200-56611800	Strong transcription	Thymus	Thymus
45	chr12:56598200-56613800	Strong transcription	Fetal Intestine Small	intestine
46	chr12:56598400-56604000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:56598400-56610600	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr12:56598400-56610600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr12:56598400-56610600	Strong transcription	HSMMtube	muscle
50	chr12:56598400-56610800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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