Variant report

Variant	rs1490691
Chromosome Location	chr10:98860760-98860761
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98858093..98860956-chr10:98957219..98958927,2	K562	blood:
2	chr10:98841269..98842045-chr10:98860672..98861381,3	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10882865	0.83[JPT][hapmap]
rs12256938	0.83[JPT][hapmap]
rs12416449	0.91[JPT][hapmap]
rs1336258	0.83[JPT][hapmap]
rs1336259	0.82[EUR][1000 genomes]
rs1490689	0.87[CHB][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1490690	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490694	0.83[JPT][hapmap]
rs1490695	0.83[JPT][hapmap]
rs2006739	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279508	0.83[JPT][hapmap]
rs2279509	0.83[JPT][hapmap]
rs2636776	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2636784	0.95[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2636786	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2636787	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2636796	0.93[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2636813	0.86[EUR][1000 genomes]
rs2636817	0.87[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2784938	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2817689	0.85[CEU][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];0.81[LWK][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2817690	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2817691	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.91[MKK][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2817693	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2817694	0.80[ASW][hapmap];0.87[CHB][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2817701	0.96[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2817703	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2817711	0.84[MEX][hapmap]
rs2817713	0.84[MEX][hapmap]
rs3000213	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4919071	0.83[JPT][hapmap]
rs7074984	0.83[JPT][hapmap]
rs7078332	0.83[JPT][hapmap]
rs7078655	0.83[JPT][hapmap]
rs7894400	0.83[JPT][hapmap]
rs7894738	0.83[JPT][hapmap]
rs7895198	0.83[JPT][hapmap]
rs7895402	0.83[JPT][hapmap]
rs7899087	0.83[JPT][hapmap]
rs7911034	0.83[JPT][hapmap]
rs902473	0.86[EUR][1000 genomes]
rs902474	0.87[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs902475	0.96[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs931451	0.87[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2758236	chr10:98789963-98962472	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759777	chr10:98789963-98962472	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1037576	chr10:98791099-98873649	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1039568	chr10:98800844-98868329	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1040262	chr10:98805336-98872134	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv895913	chr10:98854410-98884402	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1490691	DHDPSL	cis	parietal	SCAN
rs1490691	GOLGA7B	cis	cerebellum	SCAN
rs1490691	PDZD7	cis	cerebellum	SCAN
rs1490691	POLR2H	trans	cerebellum	SCAN
rs1490691	MORN4	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98841200-98869200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr10:98857000-98862400	Weak transcription	Right Atrium	heart
3	chr10:98857000-98862600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:98857000-98869200	Weak transcription	Thymus	Thymus
5	chr10:98857200-98862600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:98857200-98869000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr10:98857400-98863200	Weak transcription	Brain Anterior Caudate	brain
8	chr10:98858200-98861200	Weak transcription	Left Ventricle	heart
9	chr10:98858600-98860800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr10:98858600-98862200	Weak transcription	Brain Germinal Matrix	brain
11	chr10:98858800-98861400	Weak transcription	Right Ventricle	heart
12	chr10:98858800-98867000	Strong transcription	Fetal Thymus	thymus
13	chr10:98859000-98862200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr10:98859400-98860800	Weak transcription	Fetal Heart	heart
15	chr10:98859800-98861200	Enhancers	Fetal Brain Male	brain
16	chr10:98860400-98861600	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr10:98860400-98861800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr10:98860400-98861800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:98860600-98861200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr10:98860600-98861200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr10:98860600-98861600	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr10:98860600-98861600	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr10:98860600-98861600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr10:98860600-98861600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr10:98860600-98861600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr10:98860600-98864000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links