Variant report

Variant	rs7218724
Chromosome Location	chr17:60111468-60111469
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:60109100..60115940-chr17:60139087..60144589,10	MCF-7	breast:
2	chr17:60106228..60109334-chr17:60110578..60113962,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108510	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11079459	0.80[AFR][1000 genomes]
rs12450223	0.84[ASN][1000 genomes]
rs12450560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12451910	0.90[CEU][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs12452094	1.00[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs12600620	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12600909	0.90[CEU][hapmap];0.82[JPT][hapmap]
rs12604037	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs16945692	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16945753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16945756	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16945759	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16945801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271576	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2278812	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.84[ASN][1000 genomes]
rs2378908	0.88[GIH][hapmap];0.94[TSI][hapmap]
rs28654524	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3744434	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]
rs3809753	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3826419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410139	0.83[EUR][1000 genomes]
rs4422036	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4968408	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4968451	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap]
rs4968455	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968456	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs4968457	0.90[CEU][hapmap];0.81[JPT][hapmap]
rs4968460	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4968461	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4968462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4968463	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968464	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4968467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968468	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4968470	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4968476	0.90[CEU][hapmap]
rs4988344	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs56794817	0.81[AMR][1000 genomes]
rs57137451	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57746689	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57918684	0.82[EUR][1000 genomes]
rs58241345	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58335059	0.98[ASN][1000 genomes]
rs59080342	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs60053512	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61469058	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61658218	0.84[EUR][1000 genomes]
rs6504084	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap]
rs7221089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72843781	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs73334621	0.83[EUR][1000 genomes]
rs73336436	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8065778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8066964	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8074890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8080599	0.90[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs8081917	0.90[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs9630736	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	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	nsv1062816	chr17:60074670-60470465	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
3	esv2753884	chr17:60077852-60190630	Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	esv2755037	chr17:60086508-60386211	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7218724	MED13	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:60033000-60128400	Weak transcription	Stomach Mucosa	stomach
2	chr17:60074600-60123800	Weak transcription	Right Atrium	heart
3	chr17:60075800-60114400	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr17:60077200-60136800	Strong transcription	Fetal Thymus	thymus
5	chr17:60081800-60111600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr17:60094600-60113200	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr17:60095000-60112600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr17:60095000-60113200	Strong transcription	Duodenum Mucosa	Duodenum
9	chr17:60095800-60112600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr17:60095800-60113000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr17:60096000-60113000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr17:60097000-60113000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr17:60097000-60113000	Strong transcription	Sigmoid Colon	Sigmoid Colon
14	chr17:60098600-60112400	Strong transcription	Fetal Muscle Leg	muscle
15	chr17:60098600-60114600	Strong transcription	Placenta	Placenta
16	chr17:60098600-60139200	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr17:60098800-60111600	Strong transcription	Thymus	Thymus
18	chr17:60098800-60112600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr17:60098800-60112800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr17:60098800-60112800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr17:60098800-60113000	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr17:60098800-60113200	Strong transcription	Adipose Nuclei	Adipose
23	chr17:60098800-60135000	Strong transcription	Dnd41	blood
24	chr17:60099000-60111600	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr17:60099000-60111600	Strong transcription	Fetal Kidney	kidney
26	chr17:60099000-60111600	Strong transcription	A549	lung
27	chr17:60099000-60112800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr17:60099000-60113000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr17:60099000-60113000	Strong transcription	HepG2	liver
30	chr17:60099000-60113200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr17:60099000-60113200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr17:60099000-60113200	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr17:60099000-60113200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr17:60099000-60134200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr17:60099200-60113400	Strong transcription	K562	blood
36	chr17:60099400-60111600	Strong transcription	Fetal Intestine Large	intestine
37	chr17:60099400-60114200	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr17:60099400-60114400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:60099400-60131000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:60099400-60139000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr17:60100600-60114200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr17:60102800-60112800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:60104400-60113200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr17:60104600-60111600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr17:60104600-60112600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr17:60104800-60113200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr17:60104800-60113200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr17:60104800-60113800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr17:60105000-60113400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:60105000-60113800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links