Variant report

Variant	rs4729759
Chromosome Location	chr7:101536886-101536887
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101528188..101530830-chr7:101535885..101537732,3	K562	blood:
2	chr7:101532182..101534977-chr7:101535294..101537125,2	K562	blood:
3	chr7:101534339..101537271-chr7:101538707..101540826,3	K562	blood:
4	chr7:101534473..101537289-chr7:101541680..101543793,2	K562	blood:
5	chr7:101535565..101538438-chr7:101544906..101547711,2	K562	blood:
6	chr7:101535633..101539111-chr7:101541192..101544235,3	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10081174	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10226289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10227516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10240601	0.92[EUR][1000 genomes]
rs10241905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10242019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10255356	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10256232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259103	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10259964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261524	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264855	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264866	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271171	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10271838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10279763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532535	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534641	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12539310	0.88[CEU][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs13227531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13229243	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13236072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13241079	0.82[ASN][1000 genomes]
rs13241252	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2410921	0.89[ASN][1000 genomes]
rs28409703	0.88[ASN][1000 genomes]
rs34750675	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35065711	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4729756	0.80[ASN][1000 genomes]
rs4729760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55824493	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60656667	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72603509	0.84[AMR][1000 genomes]
rs72603510	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72603511	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72603512	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9656073	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4729759	MLL5	cis	cerebellum	SCAN
rs4729759	RINT1	cis	cerebellum	SCAN
rs4729759	ZKSCAN5	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101523200-101543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:101526000-101540400	Weak transcription	Aorta	Aorta
3	chr7:101526400-101542200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:101526800-101543000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr7:101527000-101538600	Weak transcription	Fetal Muscle Leg	muscle
6	chr7:101527000-101543000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:101527000-101543000	Weak transcription	NHEK	skin
8	chr7:101527200-101542200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:101528200-101539600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:101528600-101555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr7:101528800-101538600	Weak transcription	Dnd41	blood
12	chr7:101528800-101544000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:101529400-101539000	Weak transcription	Thymus	Thymus
14	chr7:101529400-101539400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr7:101529400-101539600	Weak transcription	Fetal Heart	heart
16	chr7:101529400-101543000	Weak transcription	Brain Substantia Nigra	brain
17	chr7:101529400-101554200	Weak transcription	Primary T cells from cord blood	blood
18	chr7:101530200-101538800	Weak transcription	Fetal Thymus	thymus
19	chr7:101530200-101539600	Weak transcription	Pancreas	Pancrea
20	chr7:101530400-101539400	Weak transcription	Lung	lung
21	chr7:101530600-101539400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr7:101530600-101559800	Weak transcription	GM12878-XiMat	blood
23	chr7:101531000-101545000	Weak transcription	Gastric	stomach
24	chr7:101531000-101548000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr7:101531400-101539400	Weak transcription	Fetal Stomach	stomach
26	chr7:101531400-101543000	Weak transcription	Placenta	Placenta
27	chr7:101531400-101554600	Weak transcription	Hela-S3	cervix
28	chr7:101533600-101539800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr7:101533800-101538800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:101533800-101539400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr7:101533800-101559000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr7:101534200-101537000	Enhancers	Monocytes-CD14+_RO01746	blood
33	chr7:101534200-101539600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr7:101534200-101546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr7:101534400-101537000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr7:101534400-101539400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:101534800-101537000	Enhancers	Fetal Brain Female	brain
38	chr7:101535000-101544800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr7:101535200-101537000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr7:101535400-101537200	Enhancers	Colon Smooth Muscle	Colon
41	chr7:101535400-101554400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr7:101535600-101537000	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr7:101535600-101538600	Weak transcription	Psoas Muscle	Psoas
44	chr7:101535600-101554200	Weak transcription	HepG2	liver
45	chr7:101535600-101554600	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr7:101535800-101539400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:101535800-101541000	Weak transcription	Fetal Kidney	kidney
48	chr7:101535800-101541200	Weak transcription	Adipose Nuclei	Adipose
49	chr7:101535800-101543200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr7:101535800-101543200	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links