Variant report

Variant	rs1029621
Chromosome Location	chr7:40865709-40865710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1006376	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1013574	0.85[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs10233069	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10235458	0.88[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10268219	0.85[LWK][hapmap]
rs10272186	0.95[CEU][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs10276629	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[AFR][1000 genomes]
rs1029620	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10951639	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1203569	0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12537964	0.86[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs13243593	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs13246232	0.86[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs17770843	0.95[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs17770991	0.85[LWK][hapmap]
rs1921743	0.95[CEU][hapmap];0.98[EUR][1000 genomes]
rs1921745	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs2108375	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2108376	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2302025	0.85[LWK][hapmap]
rs2302026	0.95[CEU][hapmap];0.99[EUR][1000 genomes]
rs2329877	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs34565813	0.93[ASN][1000 genomes]
rs34689844	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs35146091	0.80[AFR][1000 genomes]
rs35995194	0.84[ASN][1000 genomes]
rs4723979	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs59027414	0.98[EUR][1000 genomes]
rs62449401	0.81[AFR][1000 genomes]
rs62449405	0.98[EUR][1000 genomes]
rs62449407	0.98[EUR][1000 genomes]
rs6462989	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs68023334	0.81[AFR][1000 genomes]
rs6949092	0.93[ASN][1000 genomes]
rs723838	0.82[ASN][1000 genomes]
rs73125791	0.99[EUR][1000 genomes]
rs7784052	0.98[EUR][1000 genomes]
rs886831	0.80[AFR][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	nsv1030648	chr7:40218618-41032599	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv830972	chr7:40814709-40945917	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	esv1827128	chr7:40862370-40886576	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:40855600-40866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:40855800-40866200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr7:40862200-40867800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:40862200-40868200	Enhancers	HMEC	breast
5	chr7:40862800-40865800	Weak transcription	NH-A	brain
6	chr7:40863400-40866000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:40863400-40867800	Enhancers	NHEK	skin
8	chr7:40863600-40866600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:40863600-40867600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr7:40863800-40866200	Enhancers	Osteobl	bone
11	chr7:40863800-40867400	Enhancers	Aorta	Aorta
12	chr7:40864000-40869000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:40864000-40869600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:40864000-40871000	Enhancers	NHDF-Ad	bronchial
15	chr7:40864200-40865800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr7:40864600-40866200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:40864800-40866600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:40865000-40866000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr7:40865000-40866200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr7:40865000-40867600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr7:40865200-40866800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:40865200-40866800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:40865200-40866800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:40865400-40865800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:40865400-40866200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr7:40865400-40866800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr7:40865400-40867200	Enhancers	Brain Substantia Nigra	brain
28	chr7:40865400-40868200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr7:40865600-40866800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:40865600-40866800	Enhancers	HSMMtube	muscle
31	chr7:40865600-40867000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
32	chr7:40865600-40867600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr7:40865600-40868600	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links