Variant report

Variant	rs10748638
Chromosome Location	chr10:97451518-97451519
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:97414822..97416496-chr10:97449369..97451693,2	K562	blood:
2	chr10:97446799..97448496-chr10:97451292..97453225,2	K562	blood:
3	chr10:97450953..97453263-chr10:97623581..97625126,2	K562	blood:
4	chr10:97442384..97444653-chr10:97450684..97452802,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000059573	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10159941	0.85[CHB][hapmap]
rs10736093	0.89[JPT][hapmap]
rs10748634	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs10748635	0.84[CHB][hapmap]
rs10748637	0.86[CHB][hapmap]
rs10748642	0.89[JPT][hapmap]
rs10748643	0.89[JPT][hapmap]
rs10748648	0.83[JPT][hapmap]
rs10786228	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10786230	0.86[CHB][hapmap]
rs10786235	0.86[CHB][hapmap]
rs10786236	0.88[JPT][hapmap]
rs10882646	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs10882647	0.90[JPT][hapmap]
rs10882651	0.95[JPT][hapmap]
rs10882652	0.95[JPT][hapmap]
rs10882653	0.86[CHB][hapmap]
rs10882656	0.89[JPT][hapmap]
rs10882657	0.89[JPT][hapmap]
rs10882660	0.89[JPT][hapmap]
rs10882664	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10882665	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs10882670	0.86[CHB][hapmap]
rs10882675	0.84[JPT][hapmap]
rs11188414	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes]
rs11188425	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11188459	0.86[CHB][hapmap]
rs11188485	0.86[CHB][hapmap]
rs11188486	0.89[JPT][hapmap]
rs11188488	0.86[CHB][hapmap]
rs11188497	0.87[JPT][hapmap]
rs11188513	0.89[JPT][hapmap]
rs11596004	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs12244124	0.90[JPT][hapmap]
rs12244559	0.95[JPT][hapmap]
rs12262943	0.86[CHB][hapmap]
rs1342790	0.89[JPT][hapmap]
rs1342791	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs1418709	0.89[JPT][hapmap]
rs1573112	0.89[JPT][hapmap]
rs1933165	0.89[JPT][hapmap]
rs1933166	0.86[CHB][hapmap]
rs1933169	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs1953710	0.86[CHB][hapmap]
rs2051052	0.89[JPT][hapmap]
rs2153913	0.89[JPT][hapmap]
rs2153914	0.89[JPT][hapmap]
rs2211002	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2226163	0.88[JPT][hapmap]
rs2275273	0.83[ASW][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.87[AFR][1000 genomes]
rs2275759	0.89[JPT][hapmap]
rs2297788	0.95[JPT][hapmap]
rs2861147	0.89[JPT][hapmap]
rs2861148	0.87[JPT][hapmap]
rs2861149	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs2901873	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2986401	0.90[JPT][hapmap]
rs3176881	0.88[JPT][hapmap]
rs3176883	0.86[CHB][hapmap]
rs3176891	0.89[JPT][hapmap]
rs3181123	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs3181124	0.89[JPT][hapmap]
rs3181129	0.94[JPT][hapmap]
rs3181131	0.89[JPT][hapmap]
rs3750700	0.83[ASW][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.87[AFR][1000 genomes]
rs3750701	0.83[ASW][hapmap];0.95[CEU][hapmap];0.93[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3793749	0.90[JPT][hapmap]
rs3814159	0.89[JPT][hapmap]
rs3929900	0.94[JPT][hapmap]
rs3934409	0.89[JPT][hapmap]
rs3949478	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4074424	0.89[JPT][hapmap]
rs4075310	0.94[JPT][hapmap]
rs4290159	0.92[CHB][hapmap];0.88[JPT][hapmap];0.87[AFR][1000 genomes]
rs4396219	0.89[JPT][hapmap]
rs4431963	0.89[JPT][hapmap]
rs4457685	0.86[CHB][hapmap]
rs4501930	0.93[CHB][hapmap]
rs4551688	0.89[JPT][hapmap]
rs4582902	0.89[JPT][hapmap]
rs4614366	0.95[JPT][hapmap]
rs4917699	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4918950	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs4918962	0.89[JPT][hapmap]
rs4918964	0.92[CHB][hapmap]
rs496426	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs5014871	0.89[JPT][hapmap]
rs501819	0.90[JPT][hapmap]
rs535449	0.90[JPT][hapmap]
rs6584022	0.94[JPT][hapmap]
rs6584023	0.89[JPT][hapmap]
rs6584026	0.86[CHB][hapmap]
rs6584027	0.89[JPT][hapmap]
rs6584028	0.86[CHB][hapmap]
rs6584033	0.86[CHB][hapmap]
rs7067762	0.89[JPT][hapmap]
rs7069234	0.86[CHB][hapmap]
rs7071836	0.89[JPT][hapmap]
rs7073723	0.86[CHB][hapmap]
rs7074403	0.89[JPT][hapmap]
rs7077566	0.89[JPT][hapmap]
rs7081414	0.86[CHB][hapmap]
rs7086986	0.89[JPT][hapmap]
rs7088584	0.89[JPT][hapmap]
rs7092594	0.88[AFR][1000 genomes]
rs7095587	0.89[JPT][hapmap]
rs7096317	0.84[JPT][hapmap]
rs7098750	0.85[CHB][hapmap]
rs749049	0.81[MEX][hapmap];0.81[MKK][hapmap]
rs7894648	0.95[JPT][hapmap]
rs7902190	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs7905653	0.86[CHB][hapmap]
rs7909569	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs7915345	0.86[CHB][hapmap]
rs7920801	0.93[JPT][hapmap]
rs7920850	0.86[CHB][hapmap]
rs945958	0.86[CHB][hapmap];0.94[JPT][hapmap]
rs9663413	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10748638	ALDH18A1	cis	cerebellum	SCAN
rs10748638	SORBS1	cis	cerebellum	SCAN
rs10748638	RRP12	cis	parietal	SCAN
rs10748638	TCTN3	cis	lymphoblastoid	seeQTL
rs10748638	ENTPD1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97423000-97452000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr10:97427800-97452600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr10:97432800-97452000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:97433000-97451800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr10:97433800-97452600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:97434000-97452000	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr10:97434200-97452000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr10:97434400-97451600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr10:97434400-97452200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr10:97434600-97451600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr10:97434800-97451800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:97434800-97451800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr10:97435000-97452000	Strong transcription	Placenta	Placenta
14	chr10:97435600-97451600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr10:97436200-97452000	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr10:97436200-97452200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr10:97436400-97451800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr10:97437200-97451800	Strong transcription	Primary T cells from cord blood	blood
19	chr10:97437200-97452400	Strong transcription	Ovary	ovary
20	chr10:97437400-97451600	Strong transcription	Duodenum Mucosa	Duodenum
21	chr10:97437400-97451800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr10:97437400-97452000	Strong transcription	Fetal Muscle Trunk	muscle
23	chr10:97437400-97452200	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr10:97438600-97451600	Strong transcription	Stomach Smooth Muscle	stomach
25	chr10:97438800-97452000	Strong transcription	Osteobl	bone
26	chr10:97439600-97452400	Strong transcription	Fetal Muscle Leg	muscle
27	chr10:97439800-97451600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr10:97440400-97452600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr10:97440800-97451600	Strong transcription	Fetal Lung	lung
30	chr10:97442800-97452800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr10:97444000-97452600	Weak transcription	Right Ventricle	heart
32	chr10:97444600-97451800	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr10:97446200-97452400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr10:97446800-97452600	Weak transcription	Stomach Mucosa	stomach
35	chr10:97447000-97452800	Weak transcription	Pancreas	Pancrea
36	chr10:97447400-97451800	Weak transcription	Fetal Brain Male	brain
37	chr10:97447400-97452000	Weak transcription	Spleen	Spleen
38	chr10:97447400-97452200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr10:97447400-97452400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr10:97447400-97452400	Weak transcription	Brain Substantia Nigra	brain
41	chr10:97447400-97452400	Weak transcription	Fetal Heart	heart
42	chr10:97447400-97452400	Weak transcription	Rectal Smooth Muscle	rectum
43	chr10:97447400-97452600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr10:97447400-97452600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr10:97447400-97452600	Weak transcription	Brain Angular Gyrus	brain
46	chr10:97447400-97452600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr10:97447400-97452800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr10:97447400-97452800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr10:97447400-97452800	Weak transcription	Esophagus	oesophagus
50	chr10:97447400-97453000	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links