Variant report

Variant	rs4774246
Chromosome Location	chr15:57231745-57231746
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57210017..57214406-chr15:57230340..57233852,4	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1015967	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs10438332	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs11071307	0.81[CEU][hapmap]
rs11630965	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11632502	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs11636655	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs11856338	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.93[LWK][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12437976	1.00[CEU][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12440219	0.91[CEU][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12591367	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs12902058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13313455	0.81[YRI][hapmap]
rs1346880	0.86[JPT][hapmap]
rs1625176	0.82[CEU][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs1631079	0.82[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs1642927	0.82[CEU][hapmap]
rs1642929	0.84[CEU][hapmap]
rs1642935	0.86[AMR][1000 genomes]
rs1642936	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs1642937	0.86[AMR][1000 genomes]
rs1642940	0.85[CEU][hapmap];0.86[JPT][hapmap]
rs1652732	0.82[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes]
rs1652738	0.82[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs1652739	0.82[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs1652740	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs1652741	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs1657926	0.82[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16977153	0.81[YRI][hapmap]
rs169893	0.84[EUR][1000 genomes]
rs17239222	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs17819940	0.82[CEU][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap]
rs1820996	0.82[CHB][hapmap]
rs190039	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs1963831	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1968399	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1975092	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2111890	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2116067	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2116068	0.82[EUR][1000 genomes]
rs2126402	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs213152	0.87[EUR][1000 genomes]
rs213155	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs213160	0.82[CEU][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs213163	0.82[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes]
rs213166	0.82[CEU][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs213168	0.82[CEU][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2163370	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169468	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2252289	0.82[CHB][hapmap];0.86[TSI][hapmap]
rs2435905	0.86[JPT][hapmap];0.86[TSI][hapmap]
rs2439921	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2439925	0.83[AMR][1000 genomes]
rs2464427	0.82[CHB][hapmap];0.84[TSI][hapmap]
rs2464428	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs2470080	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2470081	0.82[CHB][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs2470083	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2470084	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2543675	1.00[CEU][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2566840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2566844	0.82[CEU][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes]
rs2566856	0.86[TSI][hapmap]
rs2585076	0.86[CEU][hapmap];0.80[CHD][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes]
rs2585116	0.82[CEU][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes]
rs2703588	0.82[CHB][hapmap]
rs2733187	0.82[CHB][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs28637136	0.93[ASN][1000 genomes]
rs2920270	0.82[CEU][hapmap]
rs2920272	0.86[JPT][hapmap]
rs2951900	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2951902	0.82[CHB][hapmap]
rs2957573	0.86[JPT][hapmap]
rs2957576	0.90[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs2957578	0.82[CHB][hapmap];0.90[GIH][hapmap];0.86[TSI][hapmap]
rs2957592	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs2962994	0.86[JPT][hapmap]
rs2962995	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs34373044	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4581646	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4774245	0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs4774247	0.95[ASN][1000 genomes]
rs4774900	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7162730	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7164742	0.95[CEU][hapmap];0.83[TSI][hapmap]
rs7168945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7183392	0.86[JPT][hapmap]
rs7359192	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs8023343	0.92[YRI][hapmap]
rs8029445	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs8031788	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8035485	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs8042190	0.82[CEU][hapmap]
rs9806712	0.85[CEU][hapmap];0.86[JPT][hapmap]

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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4774246	TCF12	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
3	chr15:57212600-57241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:57216400-57241800	Weak transcription	Fetal Brain Male	brain
6	chr15:57220400-57236400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:57222600-57231800	Weak transcription	HSMM	muscle
8	chr15:57222600-57233000	Weak transcription	Right Ventricle	heart
9	chr15:57222600-57250200	Weak transcription	NH-A	brain
10	chr15:57222800-57231800	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:57222800-57232600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:57222800-57240800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:57222800-57255000	Weak transcription	HMEC	breast
14	chr15:57223000-57236800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr15:57223200-57240400	Weak transcription	Aorta	Aorta
16	chr15:57224400-57231800	Weak transcription	Adipose Nuclei	Adipose
17	chr15:57224400-57231800	Weak transcription	Right Atrium	heart
18	chr15:57224400-57234400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:57224400-57235200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:57224400-57238000	Weak transcription	Fetal Lung	lung
21	chr15:57224600-57233800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:57224600-57248600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:57225000-57239400	Weak transcription	Left Ventricle	heart
24	chr15:57225000-57244200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:57225000-57249000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:57225200-57238000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr15:57226400-57234000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:57226400-57235200	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:57226400-57242000	Weak transcription	HUVEC	blood vessel
30	chr15:57226600-57234600	Weak transcription	Fetal Heart	heart
31	chr15:57227000-57233000	Weak transcription	HSMMtube	muscle
32	chr15:57227000-57249800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:57227200-57231800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:57227200-57234200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:57227200-57236800	Weak transcription	A549	lung
36	chr15:57227400-57231800	Weak transcription	Brain Hippocampus Middle	brain
37	chr15:57227600-57234000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:57227600-57234000	Weak transcription	Brain Germinal Matrix	brain
39	chr15:57227600-57235400	Weak transcription	Dnd41	blood
40	chr15:57227600-57236000	Weak transcription	Psoas Muscle	Psoas
41	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:57227800-57235200	Weak transcription	NHEK	skin
43	chr15:57228000-57232000	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr15:57228000-57233200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:57228000-57234600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:57228000-57235200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:57228000-57237600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr15:57228000-57237600	Weak transcription	Fetal Intestine Large	intestine
49	chr15:57228000-57238000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:57228000-57242400	Weak transcription	Fetal Intestine Small	intestine

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