Variant report

Variant	rs10494477
Chromosome Location	chr1:169317414-169317415
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:168572446..168573392-chr1:169317346..169318310,9	MCF-7	breast:
2	chr1:168606588..168607302-chr1:169317375..169317960,4	K562	blood:
3	chr1:168605132..168606019-chr1:169317390..169318347,3	MCF-7	breast:
4	chr1:169317063..169319375-chr1:169454243..169457078,2	K562	blood:
5	chr1:168604062..168606034-chr1:169316647..169318325,2	MCF-7	breast:
6	chr1:169315275..169317459-chr1:169319904..169321487,2	K562	blood:
7	chr1:168572454..168573380-chr1:169317397..169317940,2	K562	blood:
8	chr1:168606300..168607332-chr1:169317339..169318501,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000117479	Chromatin interaction
ENSG00000213062	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1011638	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1018832	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10458394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10489190	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10489417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs10494478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10737545	1.00[ASN][1000 genomes]
rs10800429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800431	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800432	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10800433	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10800434	1.00[ASN][1000 genomes]
rs10919085	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10919122	1.00[AFR][1000 genomes]
rs10919123	1.00[AFR][1000 genomes]
rs10919125	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10919127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10919128	1.00[ASN][1000 genomes]
rs10919130	1.00[ASN][1000 genomes]
rs10919133	1.00[ASN][1000 genomes]
rs10919134	1.00[ASN][1000 genomes]
rs10919135	1.00[ASN][1000 genomes]
rs10919144	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10919147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919149	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10919150	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10919153	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10919158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10919162	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10919165	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12021696	1.00[AFR][1000 genomes]
rs12022617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12022768	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12025397	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12025566	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12025721	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12028197	1.00[AFR][1000 genomes]
rs12028208	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12029800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12029857	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12030541	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12030810	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12031371	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12031830	1.00[ASN][1000 genomes]
rs12036426	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12037926	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12042082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12042990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044982	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12045803	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12048188	1.00[AFR][1000 genomes]
rs12401962	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12401966	1.00[AFR][1000 genomes]
rs12402774	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12405185	1.00[AFR][1000 genomes]
rs12405725	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes]
rs12408636	1.00[AFR][1000 genomes]
rs12410241	1.00[AFR][1000 genomes]
rs12410387	1.00[AFR][1000 genomes]
rs12410456	1.00[AFR][1000 genomes]
rs12567342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517742	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1517746	1.00[AFR][1000 genomes]
rs1517749	1.00[ASN][1000 genomes]
rs1517750	1.00[ASN][1000 genomes]
rs17345156	1.00[JPT][hapmap]
rs17345426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17345531	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17349677	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17518147	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs17576927	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1856302	1.00[ASN][1000 genomes]
rs2001156	1.00[AFR][1000 genomes]
rs2090514	1.00[ASN][1000 genomes]
rs2092083	1.00[AFR][1000 genomes]
rs34323371	1.00[AFR][1000 genomes]
rs3766074	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs3766100	0.83[EUR][1000 genomes]
rs3766101	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4497270	1.00[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4534447	1.00[ASN][1000 genomes]
rs4562680	1.00[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs61806987	1.00[ASN][1000 genomes]
rs72704035	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs72706084	1.00[AFR][1000 genomes]
rs7413522	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7414819	1.00[AFR][1000 genomes]
rs7522565	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7528142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7556463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs929132	1.00[ASN][1000 genomes]
rs9887925	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10494477	NME7	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
2	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr1:169296600-169324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:169303800-169317600	Weak transcription	Liver	Liver
5	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
6	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:169309400-169336400	Weak transcription	Ovary	ovary
8	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:169314800-169318200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
12	chr1:169316400-169321800	Weak transcription	HUVEC	blood vessel
13	chr1:169316600-169318000	Enhancers	Fetal Brain Male	brain
14	chr1:169316600-169318200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:169317000-169318000	Enhancers	Colon Smooth Muscle	Colon
16	chr1:169317000-169318000	Weak transcription	Fetal Intestine Large	intestine
17	chr1:169317000-169318200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:169317000-169318200	Enhancers	A549	lung
19	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
20	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr1:169317400-169317800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:169317400-169317800	Enhancers	Fetal Heart	heart
23	chr1:169317400-169318200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links