Variant report

Variant	rs10740997
Chromosome Location	chr10:22269847-22269848
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:22265820..22270074-chr10:22272130..22276008,4	K562	blood:
2	chr10:22268957..22271744-chr10:22629336..22631131,2	K562	blood:
3	chr10:22268136..22270881-chr10:22271733..22273777,2	MCF-7	breast:
4	chr10:22269767..22271640-chr10:22271920..22273622,2	MCF-7	breast:
5	chr10:22266744..22270763-chr10:22608358..22611038,3	K562	blood:

Variant related genes	Relation type
ENSG00000272366	Chromatin interaction
ENSG00000168283	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10828266	0.82[MEX][hapmap]
rs1086896	0.86[ASN][1000 genomes]
rs1086899	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11012794	0.82[MEX][hapmap]
rs2252343	0.80[ASN][1000 genomes]
rs2457954	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2487512	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs2666750	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[ASN][1000 genomes]
rs2666753	0.84[GIH][hapmap]
rs2666756	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs2666759	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2666760	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2666761	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2666762	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2666781	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs2793341	0.80[ASN][1000 genomes]
rs2793351	0.80[ASN][1000 genomes]
rs2793352	0.80[ASN][1000 genomes]
rs2807978	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2807980	0.80[ASN][1000 genomes]
rs2807982	0.80[CEU][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2807983	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2807988	0.81[CEU][hapmap];0.84[AMR][1000 genomes]
rs4146689	0.83[TSI][hapmap]
rs6650129	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6650130	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898685	1.00[CHB][hapmap]
rs7904395	0.86[ASN][1000 genomes]
rs792452	0.86[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	esv1802317	chr10:21866085-22288132	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1793816	chr10:22088054-22285371	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1048924	chr10:22177164-22296409	Enhancers Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv831808	chr10:22187850-22357814	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10740997	DNAJC1	cis	parietal	SCAN
rs10740997	TAS2R20	trans	parietal	SCAN
rs10740997	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22257000-22270600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr10:22260600-22273800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr10:22262000-22270000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr10:22262000-22274800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr10:22264600-22286000	Weak transcription	Gastric	stomach
6	chr10:22266000-22270000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr10:22266000-22278400	Weak transcription	Pancreas	Pancrea
8	chr10:22266000-22282200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr10:22266200-22270800	Weak transcription	Small Intestine	intestine
10	chr10:22266600-22270000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr10:22266800-22270000	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr10:22267600-22284400	Weak transcription	Osteobl	bone
13	chr10:22267800-22275200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr10:22268200-22270000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr10:22268200-22270600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr10:22268400-22270600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr10:22268800-22275400	Weak transcription	Fetal Intestine Small	intestine
18	chr10:22269000-22270600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr10:22269400-22270000	Enhancers	Brain Substantia Nigra	brain
20	chr10:22269400-22270000	Weak transcription	Colon Smooth Muscle	Colon
21	chr10:22269400-22270200	Enhancers	Fetal Lung	lung
22	chr10:22269400-22275000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr10:22269600-22284000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links