Variant report

Variant	rs10493544
Chromosome Location	chr1:74983835-74983836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1040070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890130	0.88[CEU][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs11210476	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11210477	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs11210478	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs12036473	0.89[CEU][hapmap]
rs12041852	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12041912	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12042908	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12142020	0.88[CEU][hapmap]
rs12566985	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1514173	0.88[CEU][hapmap]
rs1514174	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1514176	0.96[CEU][hapmap]
rs1514177	0.96[CEU][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap]
rs2344508	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3765680	0.88[CEU][hapmap]
rs3845344	0.85[CEU][hapmap]
rs3845345	0.88[CEU][hapmap];0.84[MEX][hapmap];0.81[TSI][hapmap]
rs3845347	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3894212	0.88[CEU][hapmap]
rs3895907	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4650277	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6604866	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6604867	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6604871	0.88[CEU][hapmap];0.84[MEX][hapmap]
rs6604872	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6656785	0.85[CEU][hapmap]
rs6690871	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6698622	0.88[CEU][hapmap]
rs6703637	0.88[CEU][hapmap]
rs7514705	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7520945	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7525548	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7526762	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7551507	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7553158	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7553348	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs953567	0.92[CEU][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1011745	chr1:74730942-75477618	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv535003	chr1:74730942-75477618	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1010042	chr1:74798856-75001977	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1002903	chr1:74831209-74993866	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv830248	chr1:74962391-75144458	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv525557	chr1:74977705-74991644	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv1003356	chr1:74983681-75024938	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv871900	chr1:74983835-75014195	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74978800-74989800	Weak transcription	Right Atrium	heart
2	chr1:74979000-74986400	Weak transcription	Left Ventricle	heart
3	chr1:74979000-74986800	Weak transcription	Fetal Heart	heart
4	chr1:74979600-74987800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:74980000-74987800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:74983000-74984400	Enhancers	GM12878-XiMat	blood
7	chr1:74983600-74987200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links