Variant report

Variant	rs12315732
Chromosome Location	chr12:50143637-50143638
allele	C/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	chr12:50143339-50143638	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:50143403-50143687	GM12892	blood:	n/a	n/a
3	RUNX3	chr12:50143407-50144603	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:50143198-50143715	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:50143479-50145095	K562	blood:	n/a	n/a
6	POLR2A	chr12:50143526-50145034	A549	lung:	n/a	n/a
7	NFIC	chr12:50143612-50144609	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:50143326-50145014	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:50143526-50145493	K562	blood:	n/a	n/a
10	JUN	chr12:50143426-50145488	K562	blood:	n/a	chr12:50145327-50145336 chr12:50144399-50144407 chr12:50144400-50144411

No.	Distal block	Cell Line	Cell type
1	chr12:50018757..50020272-chr12:50141476..50143680,2	K562	blood:
2	chr12:50142342..50144215-chr12:50231423..50233388,2	K562	blood:
3	chr12:50030201..50031969-chr12:50143354..50146117,2	K562	blood:
4	chr12:50142752..50145043-chr12:50235081..50237094,3	K562	blood:
5	chr12:50099618..50102364-chr12:50142236..50145462,3	K562	blood:
6	chr12:50030639..50033047-chr12:50142456..50143972,2	MCF-7	breast:

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000139644	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000161791	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10161088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10219602	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1078216	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169108	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11169121	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169128	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169129	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169130	1.00[CEU][hapmap];0.84[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11169132	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11169140	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs11503899	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12304910	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12306114	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12306565	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12308567	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12309717	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12314676	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12321910	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12321935	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2278068	1.00[CHB][hapmap]
rs28654319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755804	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35275181	1.00[CEU][hapmap]
rs56784440	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57144906	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58250762	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59511398	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59811112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7136772	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7136990	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73306854	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73306885	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73309015	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 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	chr12:50136600-50146400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:50136800-50144200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr12:50136800-50146600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:50137000-50143800	Weak transcription	Colonic Mucosa	Colon
5	chr12:50137000-50146200	Weak transcription	HSMMtube	muscle
6	chr12:50137000-50147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:50137200-50146200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:50137200-50152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:50137400-50146400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr12:50137400-50146400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr12:50137400-50146600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:50137400-50150800	Weak transcription	Fetal Brain Male	brain
13	chr12:50137600-50146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr12:50137800-50143800	Weak transcription	Fetal Stomach	stomach
15	chr12:50137800-50144200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr12:50137800-50146200	Weak transcription	Fetal Kidney	kidney
17	chr12:50138000-50143800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:50138200-50146400	Weak transcription	Fetal Brain Female	brain
19	chr12:50138400-50144000	Weak transcription	Fetal Lung	lung
20	chr12:50138600-50143800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:50138600-50143800	Weak transcription	Small Intestine	intestine
22	chr12:50138600-50144000	Weak transcription	Esophagus	oesophagus
23	chr12:50138600-50144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:50138600-50146400	Weak transcription	Brain Germinal Matrix	brain
25	chr12:50138800-50143800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr12:50138800-50143800	Weak transcription	NHLF	lung
27	chr12:50138800-50144000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:50139000-50143800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr12:50139000-50143800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr12:50139000-50143800	Weak transcription	Aorta	Aorta
31	chr12:50139000-50143800	Weak transcription	HUVEC	blood vessel
32	chr12:50139000-50144000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr12:50139000-50146200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr12:50139000-50146600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr12:50139200-50143800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:50139200-50143800	Weak transcription	Fetal Muscle Leg	muscle
37	chr12:50139600-50143800	Strong transcription	Primary B cells from cord blood	blood
38	chr12:50140600-50144000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:50140800-50144600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:50141000-50144000	Strong transcription	A549	lung
41	chr12:50141000-50146200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:50141400-50144000	Genic enhancers	NHEK	skin
43	chr12:50141400-50144200	Genic enhancers	Fetal Intestine Small	intestine
44	chr12:50141400-50146800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:50141600-50143800	Enhancers	Primary T cells fromperipheralblood	blood
46	chr12:50141600-50143800	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr12:50141600-50144000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr12:50141800-50144000	Enhancers	Liver	Liver
49	chr12:50141800-50144600	Enhancers	Right Atrium	heart
50	chr12:50142000-50144000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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