Variant report

Variant	rs10732287
Chromosome Location	chr1:169276816-169276817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169275275..169277238-chr1:169338409..169341241,2	K562	blood:
2	chr1:169276766..169278589-chr1:169293120..169295874,2	K562	blood:
3	chr1:169276344..169278316-chr1:169279851..169282220,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235575	Chromatin interaction
ENSG00000143156	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10081960	0.83[ASN][1000 genomes]
rs1018831	0.82[JPT][hapmap]
rs1040502	1.00[CHB][hapmap]
rs10429893	0.82[JPT][hapmap]
rs10800408	0.82[JPT][hapmap]
rs10800424	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10800425	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10800435	0.82[JPT][hapmap]
rs10800438	0.82[JPT][hapmap]
rs10800440	0.82[JPT][hapmap]
rs10919124	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10919174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1200063	0.87[ASN][1000 genomes]
rs1200079	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1200085	0.82[JPT][hapmap]
rs1200160	1.00[CHB][hapmap]
rs1200164	0.82[JPT][hapmap]
rs1208135	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1208327	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1208370	0.82[JPT][hapmap]
rs1208377	0.87[CHD][hapmap]
rs12086665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12137282	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12138150	0.83[ASN][1000 genomes]
rs12752748	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1400836	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs1400839	0.81[ASN][1000 genomes]
rs1517744	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1517747	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1591733	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs16861990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17345107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17349222	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1829286	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856303	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1892094	1.00[CHB][hapmap]
rs1983546	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2037250	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2066000	0.81[ASN][1000 genomes]
rs2138898	0.82[JPT][hapmap]
rs2152979	0.81[ASN][1000 genomes]
rs2176473	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2179490	0.83[ASN][1000 genomes]
rs2211017	0.81[ASN][1000 genomes]
rs2420008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3766044	1.00[CHB][hapmap]
rs3766057	0.82[JPT][hapmap]
rs3766095	0.82[JPT][hapmap]
rs3905328	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs4264046	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs4454599	0.81[ASN][1000 genomes]
rs4656178	0.83[ASN][1000 genomes]
rs4656183	0.82[JPT][hapmap]
rs4656672	0.82[JPT][hapmap]
rs61803315	0.83[ASN][1000 genomes]
rs61803316	0.83[ASN][1000 genomes]
rs6427185	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs6656822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6662237	0.81[ASN][1000 genomes]
rs6691226	0.81[ASN][1000 genomes]
rs7415756	0.82[JPT][hapmap]
rs7521582	0.87[CHD][hapmap]
rs7522760	0.83[ASN][1000 genomes]
rs7533257	0.87[CHD][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs7540067	1.00[CHB][hapmap]
rs7542713	0.83[ASN][1000 genomes]
rs754550	1.00[CHB][hapmap]
rs754551	1.00[CHB][hapmap]
rs7552323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs994986	0.81[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	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	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs10732287	KIFAP3	cis	cerebellum	SCAN
rs10732287	NME7	cis	Esophagus Muscularis	GTEx
rs10732287	NME7	cis	multi-tissue	Pritchard
rs10732287	F5	cis	cerebellum	SCAN
rs10732287	NME7	cis	parietal	SCAN
rs10732287	SCYL3	cis	parietal	SCAN
rs10732287	SELP	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169252800-169278600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:169252800-169278800	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:169253600-169280600	Weak transcription	Fetal Kidney	kidney
4	chr1:169254800-169281000	Weak transcription	Dnd41	blood
5	chr1:169256800-169278600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:169257600-169284800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:169257800-169281200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr1:169258800-169277400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:169259200-169278600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:169259400-169278600	Weak transcription	Adipose Nuclei	Adipose
11	chr1:169259600-169278600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:169259600-169294400	Weak transcription	Pancreas	Pancrea
13	chr1:169260400-169310400	Weak transcription	Fetal Stomach	stomach
14	chr1:169260600-169278800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:169262800-169278600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:169263000-169278600	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr1:169264000-169281400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:169264200-169278600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:169264400-169294400	Weak transcription	Left Ventricle	heart
20	chr1:169265000-169278600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:169265000-169320400	Weak transcription	Aorta	Aorta
22	chr1:169265200-169277200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:169265200-169278400	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:169265200-169281200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:169265400-169281200	Weak transcription	NHDF-Ad	bronchial
26	chr1:169265800-169281000	Weak transcription	Fetal Intestine Large	intestine
27	chr1:169266200-169278600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:169266200-169280200	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:169267000-169278400	Weak transcription	Brain Anterior Caudate	brain
30	chr1:169267000-169281200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr1:169267800-169281200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:169268000-169278600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:169269000-169278800	Weak transcription	Fetal Brain Female	brain
34	chr1:169269000-169281200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:169269200-169281400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:169269400-169281600	Weak transcription	HUVEC	blood vessel
37	chr1:169269600-169281000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:169270200-169278600	Weak transcription	Brain Substantia Nigra	brain
39	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr1:169270400-169277200	Weak transcription	Colon Smooth Muscle	Colon
41	chr1:169270400-169278600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr1:169271800-169278600	Weak transcription	Primary B cells from cord blood	blood
43	chr1:169271800-169297200	Weak transcription	Psoas Muscle	Psoas
44	chr1:169272000-169277400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr1:169272000-169278800	Weak transcription	Fetal Brain Male	brain
46	chr1:169273400-169278200	Weak transcription	Brain Germinal Matrix	brain
47	chr1:169273600-169281000	Weak transcription	A549	lung
48	chr1:169273600-169312400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:169273800-169279800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr1:169274800-169277000	Strong transcription	Duodenum Smooth Muscle	Duodenum

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