Variant report

Variant	rs11765962
Chromosome Location	chr7:140126507-140126508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10216203	0.96[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs10224992	0.91[JPT][hapmap];0.87[EUR][1000 genomes]
rs10226064	0.87[EUR][1000 genomes]
rs10229678	0.87[EUR][1000 genomes]
rs10231547	0.87[EUR][1000 genomes]
rs10243155	0.84[EUR][1000 genomes]
rs10244642	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10256899	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10257079	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10258350	0.92[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs10267810	0.84[EUR][1000 genomes]
rs10269611	0.92[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs10270875	0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs10272040	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10272047	0.87[EUR][1000 genomes]
rs10273061	0.83[EUR][1000 genomes]
rs10275127	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10275142	0.87[EUR][1000 genomes]
rs10278060	0.84[EUR][1000 genomes]
rs10279172	0.84[EUR][1000 genomes]
rs10280145	0.87[EUR][1000 genomes]
rs11760895	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11766079	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11974068	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11978135	0.85[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.85[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12216619	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13438384	0.84[EUR][1000 genomes]
rs13438583	0.84[EUR][1000 genomes]
rs17161542	0.88[EUR][1000 genomes]
rs17161569	0.92[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs1969394	0.84[EUR][1000 genomes]
rs2001941	0.83[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes]
rs2272096	0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs2363824	0.88[EUR][1000 genomes]
rs2363826	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2363828	0.87[EUR][1000 genomes]
rs28412759	0.88[EUR][1000 genomes]
rs28439514	0.87[EUR][1000 genomes]
rs28538447	0.88[EUR][1000 genomes]
rs28553284	1.00[EUR][1000 genomes]
rs28563126	0.83[EUR][1000 genomes]
rs28667371	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28699169	0.83[EUR][1000 genomes]
rs28784908	0.84[EUR][1000 genomes]
rs28785875	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28832645	0.87[EUR][1000 genomes]
rs2885922	0.86[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28880113	0.84[EUR][1000 genomes]
rs35747234	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4385389	0.88[EUR][1000 genomes]
rs4424177	0.92[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs4427086	0.84[EUR][1000 genomes]
rs4431522	0.83[EUR][1000 genomes]
rs55714045	0.84[EUR][1000 genomes]
rs55833852	0.87[EUR][1000 genomes]
rs55961611	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56059991	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56769703	0.87[EUR][1000 genomes]
rs58076938	0.84[EUR][1000 genomes]
rs58647694	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59814044	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60137728	0.84[EUR][1000 genomes]
rs61577108	0.84[EUR][1000 genomes]
rs62490410	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62490429	0.87[EUR][1000 genomes]
rs62490449	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6464773	0.92[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs6464779	0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs6951446	0.87[EUR][1000 genomes]
rs6962593	0.92[GIH][hapmap];0.82[EUR][1000 genomes]
rs6962710	0.89[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs6963738	0.87[EUR][1000 genomes]
rs6964170	0.81[EUR][1000 genomes]
rs6966049	0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs6966056	0.84[EUR][1000 genomes]
rs6968931	0.90[EUR][1000 genomes]
rs6973069	0.99[EUR][1000 genomes]
rs6975307	0.87[EUR][1000 genomes]
rs7777404	0.84[EUR][1000 genomes]
rs7779827	0.84[EUR][1000 genomes]
rs7784093	0.88[AFR][1000 genomes]
rs7784558	0.87[EUR][1000 genomes]
rs7785094	0.89[GIH][hapmap]
rs7786776	0.84[EUR][1000 genomes]
rs7787217	0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs7789557	0.87[EUR][1000 genomes]
rs7790232	0.84[EUR][1000 genomes]
rs7800959	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7805365	0.87[EUR][1000 genomes]
rs7808589	0.84[EUR][1000 genomes]
rs7811669	0.81[EUR][1000 genomes]
rs9648837	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9692138	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522190	chr7:140066411-140130663	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv464734	chr7:140108096-140217670	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv608500	chr7:140108096-140217670	Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Weak transcription 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	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11765962	LUC7L2	cis	cerebellum	SCAN
rs11765962	JHDM1D	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140104200-140133400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr7:140104600-140127800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:140104800-140128200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:140104800-140129000	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr7:140105000-140126600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:140105000-140128200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr7:140105000-140132400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:140113800-140128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:140114000-140127400	Weak transcription	Fetal Intestine Small	intestine
10	chr7:140117800-140126600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr7:140117800-140129600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr7:140117800-140130600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr7:140118000-140127800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr7:140118000-140129600	Weak transcription	Colonic Mucosa	Colon
15	chr7:140125000-140126600	Strong transcription	Primary T cells from cord blood	blood
16	chr7:140125000-140127000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:140125000-140127400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:140125600-140126600	Strong transcription	Gastric	stomach
19	chr7:140125800-140126600	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr7:140125800-140126600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr7:140125800-140126600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:140125800-140126600	Strong transcription	Pancreas	Pancrea
23	chr7:140125800-140126800	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:140126000-140126600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr7:140126000-140126600	Strong transcription	Fetal Intestine Large	intestine
26	chr7:140126000-140126600	Strong transcription	Rectal Mucosa Donor 29	rectum
27	chr7:140126000-140126600	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr7:140126200-140127400	Weak transcription	Fetal Stomach	stomach
29	chr7:140126200-140127800	Weak transcription	Spleen	Spleen
30	chr7:140126400-140128200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr7:140126400-140129800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr7:140126400-140135200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr7:140126400-140176600	Weak transcription	Right Atrium	heart

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