Variant report

Variant	rs3744434
Chromosome Location	chr17:59989126-59989127
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:59988596..59990482-chr17:59998557..60001348,2	MCF-7	breast:
2	chr17:59984827..59990978-chr17:60003230..60006260,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108506	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10512492	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes]
rs11079459	0.88[AMR][1000 genomes]
rs12450560	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs12451910	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12452094	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12452732	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12600620	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12600909	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12604037	0.81[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16945692	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16945753	0.90[CEU][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes]
rs16945756	0.86[AMR][1000 genomes]
rs16945759	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes]
rs16945801	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs2271576	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2278812	0.88[GIH][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap]
rs2378908	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs3809753	0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs3826419	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4422036	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs4968408	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968451	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4968452	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4968454	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968455	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4968456	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4968457	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968459	0.80[ASN][1000 genomes]
rs4968460	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968461	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968462	0.82[JPT][hapmap]
rs4968463	0.95[AMR][1000 genomes]
rs4968467	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968468	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs4968476	0.81[CEU][hapmap]
rs4988344	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56794817	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58085921	0.81[ASN][1000 genomes]
rs58241345	0.82[AMR][1000 genomes]
rs58624595	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59080342	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61169879	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61658218	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6504084	0.81[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs7218724	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs7221089	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap]
rs73332565	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73332580	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73332598	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73334621	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8065778	0.90[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes]
rs8066964	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes]
rs8074890	0.90[CEU][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes]
rs8080599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8081917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9630735	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9630736	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][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	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv916786	chr17:59890834-60103687	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3744434	MED13	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59941400-60004400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:59941400-60004400	Weak transcription	Aorta	Aorta
3	chr17:59941400-60004400	Weak transcription	Pancreas	Pancrea
4	chr17:59941600-60003600	Weak transcription	Stomach Mucosa	stomach
5	chr17:59941600-60004400	Weak transcription	Colonic Mucosa	Colon
6	chr17:59942600-60002800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr17:59943600-59989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:59946600-59989200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:59951400-59992200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:59951600-59989600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr17:59954400-60003800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr17:59959000-59996800	Weak transcription	Gastric	stomach
13	chr17:59959600-60003600	Weak transcription	Fetal Heart	heart
14	chr17:59963400-59989600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:59963800-59989600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr17:59966000-60004200	Weak transcription	Psoas Muscle	Psoas
17	chr17:59966200-59998000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr17:59974200-59989600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr17:59974200-59993000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:59974400-59989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr17:59974800-59989400	Strong transcription	Fetal Muscle Trunk	muscle
22	chr17:59975000-59989400	Strong transcription	Fetal Thymus	thymus
23	chr17:59975400-59991800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:59975400-60004600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr17:59975600-59989600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr17:59975600-59991000	Strong transcription	Fetal Stomach	stomach
27	chr17:59976200-59992400	Strong transcription	HepG2	liver
28	chr17:59977200-59989600	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr17:59977400-59989600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr17:59977400-59989600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:59978400-59989600	Strong transcription	Dnd41	blood
32	chr17:59978600-60004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:59979000-59989600	Strong transcription	Primary T cells from cord blood	blood
34	chr17:59979000-59989600	Strong transcription	Liver	Liver
35	chr17:59979000-59989600	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr17:59979400-59989200	Strong transcription	HSMM	muscle
37	chr17:59980200-60003600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr17:59980800-59989400	Strong transcription	Fetal Brain Female	brain
39	chr17:59981600-59989600	Strong transcription	Primary hematopoietic stem cells	blood
40	chr17:59982000-59992400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr17:59982200-59989600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr17:59982600-60001400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr17:59982600-60003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr17:59982800-59989600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr17:59983000-59989400	Strong transcription	Primary B cells from cord blood	blood
46	chr17:59983000-59997000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr17:59983200-59989400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr17:59983200-59989600	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr17:59983200-59992200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr17:59983400-59989600	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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