Variant report

Variant	rs4729760
Chromosome Location	chr7:101543497-101543498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:101541469..101544345-chr7:101547071..101549118,2	MCF-7	breast:
2	chr7:101535633..101539111-chr7:101541192..101544235,3	MCF-7	breast:
3	chr7:101460117..101462144-chr7:101543325..101545427,2	K562	blood:
4	chr7:101522402..101527695-chr7:101541882..101547914,5	MCF-7	breast:
5	chr7:101541658..101544389-chr7:101544721..101546512,2	K562	blood:
6	chr7:101534473..101537289-chr7:101541680..101543793,2	K562	blood:
7	chr7:101542354..101543995-chr7:101557811..101560799,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10081174	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10226289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10227516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10240601	0.96[EUR][1000 genomes]
rs10241905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10242019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10255356	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10256232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10259103	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10259964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10261524	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10264844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10264855	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10264866	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]
rs10271171	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10271610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271838	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]
rs10279763	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532535	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534641	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539310	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs13227531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13229243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13241079	0.81[ASN][1000 genomes]
rs13241252	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2410921	0.88[ASN][1000 genomes]
rs28409703	0.87[ASN][1000 genomes]
rs34750675	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35065711	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4729759	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	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60656667	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72603509	0.82[AMR][1000 genomes]
rs72603510	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72603511	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72603512	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9656073	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	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
4	nsv482846	chr7:101539981-101707666	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4729760	RINT1	cis	cerebellum	SCAN
rs4729760	ZKSCAN5	cis	parietal	SCAN
rs4729760	MLL5	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101528600-101555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:101528800-101544000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:101529400-101554200	Weak transcription	Primary T cells from cord blood	blood
4	chr7:101530600-101559800	Weak transcription	GM12878-XiMat	blood
5	chr7:101531000-101545000	Weak transcription	Gastric	stomach
6	chr7:101531000-101548000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr7:101531400-101554600	Weak transcription	Hela-S3	cervix
8	chr7:101533800-101559000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:101534200-101546600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr7:101535000-101544800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:101535400-101554400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr7:101535600-101554200	Weak transcription	HepG2	liver
13	chr7:101535600-101554600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr7:101535800-101555200	Weak transcription	Liver	Liver
15	chr7:101535800-101555600	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:101536000-101543600	Weak transcription	A549	lung
17	chr7:101536800-101543800	Weak transcription	Brain Germinal Matrix	brain
18	chr7:101537000-101543600	Weak transcription	Ovary	ovary
19	chr7:101537000-101547600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr7:101537000-101547600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr7:101537000-101554400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr7:101537000-101554600	Weak transcription	Fetal Intestine Large	intestine
23	chr7:101537600-101559000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr7:101539600-101548800	Weak transcription	Thymus	Thymus
25	chr7:101540000-101545400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr7:101540000-101546400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr7:101540000-101555600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr7:101540200-101559200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:101540400-101548200	Weak transcription	Spleen	Spleen
30	chr7:101540400-101555200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:101540400-101559200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr7:101540600-101547200	Strong transcription	Fetal Intestine Small	intestine
33	chr7:101540800-101548600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr7:101541200-101544000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr7:101541200-101544800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:101541200-101544800	Weak transcription	K562	blood
37	chr7:101541400-101554400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr7:101541400-101555000	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr7:101541400-101555000	Weak transcription	Fetal Thymus	thymus
40	chr7:101541600-101545200	Weak transcription	Adipose Nuclei	Adipose
41	chr7:101541800-101544000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr7:101541800-101545000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:101541800-101548400	Weak transcription	Primary B cells from cord blood	blood
44	chr7:101542200-101546000	Enhancers	Fetal Heart	heart
45	chr7:101542400-101543800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr7:101542400-101544000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:101542400-101545000	Enhancers	Fetal Brain Male	brain
48	chr7:101542400-101555600	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr7:101542600-101543600	Weak transcription	Fetal Stomach	stomach
50	chr7:101542600-101558000	Weak transcription	Dnd41	blood

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