Variant report

Variant	rs501054
Chromosome Location	chr11:57561106-57561107
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:57554543..57556933-chr11:57559268..57561458,2	MCF-7	breast:
2	chr11:57560773..57562885-chr11:57566656..57568197,2	K562	blood:
3	chr11:57529656..57532573-chr11:57561003..57562915,2	MCF-7	breast:
4	chr11:57548767..57550342-chr11:57559467..57561376,2	K562	blood:

Variant related genes	Relation type
ENSG00000198561	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10896634	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11229087	0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11229115	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1267146	0.86[ASN][1000 genomes]
rs12793139	0.89[JPT][hapmap]
rs1424752	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2848445	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs479573	0.83[ASN][1000 genomes]
rs480933	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs483030	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs486995	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs491719	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs492131	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs501738	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs503037	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs504311	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs504921	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs507946	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs509564	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs511708	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs515939	0.89[ASN][1000 genomes]
rs517638	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs518804	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs523985	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs527140	1.00[ASW][hapmap];0.86[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs530094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs536673	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537627	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs540234	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs541245	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs544446	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs549022	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs549279	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs558653	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs567017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577741	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs580223	0.84[EUR][1000 genomes]
rs581217	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58132137	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594233	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604094	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604344	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs608648	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609596	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs612688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61888873	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61888880	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs624759	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs627816	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs628100	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs636807	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs638864	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs640767	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs645097	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs647264	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs656227	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658183	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs669433	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs669950	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs675154	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676205	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs685110	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs694131	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs694261	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7108113	0.81[ASN][1000 genomes]
rs72928102	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs96894	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs501054	MED19	Cis_1M	lymphoblastoid	RTeQTL
rs501054	YPEL4	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57546800-57564000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr11:57554800-57561600	Enhancers	Small Intestine	intestine
3	chr11:57555400-57563200	Weak transcription	Fetal Brain Male	brain
4	chr11:57555600-57562800	Weak transcription	Ovary	ovary
5	chr11:57556000-57562400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr11:57556000-57562400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:57556000-57567800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:57556200-57561200	Weak transcription	NHDF-Ad	bronchial
9	chr11:57556400-57587800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:57556600-57563000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:57557200-57561400	Genic enhancers	Fetal Intestine Large	intestine
12	chr11:57557200-57561600	Genic enhancers	Fetal Intestine Small	intestine
13	chr11:57557200-57561800	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr11:57557200-57566200	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr11:57557200-57566200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:57558200-57561600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:57558400-57562600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr11:57558400-57567200	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:57558400-57567400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:57558600-57561600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr11:57558600-57561600	Genic enhancers	Liver	Liver
22	chr11:57558600-57561600	Genic enhancers	Colon Smooth Muscle	Colon
23	chr11:57558600-57561600	Genic enhancers	Fetal Muscle Leg	muscle
24	chr11:57558600-57567200	Strong transcription	Fetal Brain Female	brain
25	chr11:57558800-57563000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr11:57559000-57561200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr11:57559000-57561400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr11:57559200-57561200	Flanking Active TSS	Primary B cells from cord blood	blood
29	chr11:57559200-57561200	Genic enhancers	Osteobl	bone
30	chr11:57559400-57561200	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr11:57559400-57561200	Genic enhancers	HSMM	muscle
32	chr11:57559400-57561200	Genic enhancers	HSMMtube	muscle
33	chr11:57559400-57561400	Flanking Active TSS	Primary T cells from cord blood	blood
34	chr11:57559400-57561400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr11:57559400-57571000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr11:57559600-57562000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr11:57559600-57564000	Weak transcription	Psoas Muscle	Psoas
38	chr11:57559600-57564600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:57559800-57561400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr11:57559800-57561400	Enhancers	Dnd41	blood
41	chr11:57559800-57562600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:57559800-57563000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:57559800-57563000	Weak transcription	Right Ventricle	heart
44	chr11:57559800-57566600	Strong transcription	Fetal Stomach	stomach
45	chr11:57559800-57566800	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:57560000-57561200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr11:57560000-57561200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr11:57560000-57561200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:57560000-57561200	Weak transcription	Right Atrium	heart
50	chr11:57560000-57561200	Weak transcription	Spleen	Spleen

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