Variant report

Variant	rs4968451
Chromosome Location	chr17:59927307-59927308
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:59700536..59703582-chr17:59926981..59930844,3	MCF-7	breast:
2	chr17:59926844..59927487-chr17:59936864..59937521,2	MCF-7	breast:
3	chr17:59914601..59917042-chr17:59925140..59928901,4	MCF-7	breast:
4	chr17:59926015..59928593-chr17:59929394..59932297,2	K562	blood:
5	chr16:84771847..84772515-chr17:59926819..59927535,2	MCF-7	breast:
6	chr17:59923631..59927756-chr20:55841181..55844578,4	MCF-7	breast:
7	chr17:59926033..59928047-chr20:55791254..55794077,2	MCF-7	breast:
8	chr17:59727177..59731742-chr17:59925702..59928839,4	MCF-7	breast:
9	chr17:59922363..59930982-chr17:59932743..59942161,16	K562	blood:
10	chr17:59923960..59927363-chr20:60638070..60642811,4	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBX4-3	chr17:59927233-59927465	ucExp_420_+

No data

Variant related genes	Relation type
ENSG00000101144	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000265306	Chromatin interaction
ENSG00000130699	Chromatin interaction
ENSG00000226308	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10512492	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs12451910	1.00[CEU][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12452094	0.90[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12452732	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12452742	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12453644	0.84[EUR][1000 genomes]
rs12600909	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12601269	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12604037	0.81[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes]
rs16945692	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16945753	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs16945759	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[YRI][hapmap]
rs16945801	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs2271576	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2278812	0.88[GIH][hapmap];0.93[MEX][hapmap]
rs2378908	0.84[CHD][hapmap];0.88[GIH][hapmap];0.87[TSI][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes]
rs3744434	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]
rs4968408	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968452	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4968454	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968455	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4968456	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4968457	1.00[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4968460	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4968461	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes]
rs4968462	0.87[YRI][hapmap]
rs4968463	0.81[AMR][1000 genomes]
rs4988344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56794817	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs58624595	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59080342	0.83[AMR][1000 genomes]
rs61169879	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61658218	0.85[AMR][1000 genomes]
rs7218724	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[YRI][hapmap]
rs7221089	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap]
rs73332565	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73332580	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73332598	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73334621	0.85[AMR][1000 genomes]
rs8065778	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs8066964	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap]
rs8074890	0.90[CEU][hapmap];0.87[YRI][hapmap]
rs8080599	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8081917	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9630735	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9630736	0.90[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv575842	chr17:59812748-59927307	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	70 gene(s)	inside rSNPs	diseases
3	nsv908675	chr17:59835864-59937286	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	67 gene(s)	inside rSNPs	diseases
4	nsv575843	chr17:59869081-59935723	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	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
rs4968451	MED13	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59870400-59933400	Weak transcription	Fetal Intestine Large	intestine
2	chr17:59884200-59933200	Weak transcription	K562	blood
3	chr17:59898800-59939600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr17:59898800-59939800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:59904800-59933200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:59905400-59931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr17:59905800-59939000	Weak transcription	Primary T cells from cord blood	blood
8	chr17:59906200-59940200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:59911600-59937800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr17:59911800-59939000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:59912000-59938400	Weak transcription	HUVEC	blood vessel
12	chr17:59912200-59939200	Weak transcription	HSMM	muscle
13	chr17:59912200-59939800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr17:59912400-59931400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr17:59912400-59931400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr17:59912400-59938600	Weak transcription	NHDF-Ad	bronchial
17	chr17:59912400-59938600	Weak transcription	NHEK	skin
18	chr17:59912400-59939400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr17:59912400-59940000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:59912400-59940400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr17:59914600-59932600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:59914600-59938600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr17:59916400-59931400	Strong transcription	Dnd41	blood
24	chr17:59916600-59938600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr17:59917800-59939200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr17:59918000-59939000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr17:59918800-59927400	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:59919200-59927400	Strong transcription	A549	lung
29	chr17:59919200-59928000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr17:59919200-59928000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:59919400-59928400	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr17:59919800-59934600	Weak transcription	Ovary	ovary
33	chr17:59920400-59940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr17:59920600-59930600	Strong transcription	Fetal Thymus	thymus
35	chr17:59921200-59939800	Weak transcription	Thymus	Thymus
36	chr17:59921600-59927400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr17:59921600-59940000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr17:59922000-59937800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr17:59922200-59933000	Weak transcription	HMEC	breast
40	chr17:59922200-59938400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:59922200-59939000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:59922600-59931600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr17:59923200-59928800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr17:59923200-59932200	Weak transcription	NH-A	brain
45	chr17:59923200-59938400	Weak transcription	Osteobl	bone
46	chr17:59923200-59939800	Weak transcription	Fetal Muscle Leg	muscle
47	chr17:59923400-59929200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr17:59923600-59940200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr17:59924600-59930000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr17:59924600-59930600	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links