Variant report

Variant	rs2001941
Chromosome Location	chr7:140117562-140117563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10216203	0.90[CHB][hapmap]
rs10224992	0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs10226064	0.82[EUR][1000 genomes]
rs10229678	0.82[EUR][1000 genomes]
rs10231547	0.82[EUR][1000 genomes]
rs10244642	0.94[EUR][1000 genomes]
rs10256899	0.85[EUR][1000 genomes]
rs10257079	0.83[EUR][1000 genomes]
rs10258350	0.90[CHB][hapmap]
rs10269611	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[EUR][1000 genomes]
rs10270875	0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs10272040	0.82[EUR][1000 genomes]
rs10272047	0.82[EUR][1000 genomes]
rs10275127	0.83[EUR][1000 genomes]
rs10275142	0.82[EUR][1000 genomes]
rs10280145	0.82[EUR][1000 genomes]
rs11760895	0.86[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs11765962	0.94[EUR][1000 genomes]
rs11766079	0.80[EUR][1000 genomes]
rs11974068	0.85[EUR][1000 genomes]
rs11978135	0.81[JPT][hapmap];0.83[EUR][1000 genomes]
rs12216619	0.83[EUR][1000 genomes]
rs17161542	0.83[EUR][1000 genomes]
rs17161569	0.80[EUR][1000 genomes]
rs2272096	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2363824	0.83[EUR][1000 genomes]
rs2363826	0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs2363828	0.82[EUR][1000 genomes]
rs28412759	0.83[EUR][1000 genomes]
rs28439514	0.82[EUR][1000 genomes]
rs28538447	0.83[EUR][1000 genomes]
rs28553284	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28667371	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28785875	0.83[EUR][1000 genomes]
rs28832645	0.82[EUR][1000 genomes]
rs2885922	0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs35747234	0.83[EUR][1000 genomes]
rs4385389	0.83[EUR][1000 genomes]
rs4424177	0.90[CHB][hapmap]
rs55833852	0.82[EUR][1000 genomes]
rs55961611	0.83[EUR][1000 genomes]
rs56059991	0.80[EUR][1000 genomes]
rs56769703	0.82[EUR][1000 genomes]
rs58647694	0.80[EUR][1000 genomes]
rs59814044	0.85[EUR][1000 genomes]
rs62490410	0.94[EUR][1000 genomes]
rs62490429	0.82[EUR][1000 genomes]
rs62490449	0.80[EUR][1000 genomes]
rs6464773	0.90[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs6464779	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs6951446	0.82[EUR][1000 genomes]
rs6962710	0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes]
rs6963738	0.82[EUR][1000 genomes]
rs6966049	0.90[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs6968931	0.85[EUR][1000 genomes]
rs6973069	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6975307	0.82[EUR][1000 genomes]
rs7784558	0.82[EUR][1000 genomes]
rs7787217	0.90[CHB][hapmap]
rs7789557	0.82[EUR][1000 genomes]
rs7800959	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7805365	0.82[EUR][1000 genomes]
rs7811669	0.81[EUR][1000 genomes]
rs9648837	0.83[EUR][1000 genomes]
rs9692138	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022919	chr7:140043299-140120546	Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	esv2762706	chr7:140054170-140119629	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
rs2001941	JHDM1D	cis	cerebellum	SCAN
rs2001941	LUC7L2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:140104200-140125800	Weak transcription	Right Atrium	heart
2	chr7:140104200-140133400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:140104400-140117800	Weak transcription	Colonic Mucosa	Colon
4	chr7:140104600-140127800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr7:140104800-140125600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr7:140104800-140125600	Weak transcription	Gastric	stomach
7	chr7:140104800-140125800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr7:140104800-140126000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr7:140104800-140126000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr7:140104800-140128200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr7:140104800-140129000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr7:140105000-140119000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr7:140105000-140126600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:140105000-140128200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:140105000-140132400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr7:140106800-140117600	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:140113200-140125800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr7:140113800-140128200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr7:140114000-140125600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:140114000-140127400	Weak transcription	Fetal Intestine Small	intestine
21	chr7:140114600-140125800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr7:140114600-140125800	Weak transcription	Spleen	Spleen
23	chr7:140114800-140125800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr7:140115400-140125000	Weak transcription	Primary T cells from cord blood	blood
25	chr7:140115600-140117800	Enhancers	Pancreas	Pancrea
26	chr7:140116200-140118200	Enhancers	Fetal Thymus	thymus
27	chr7:140116400-140117800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr7:140116400-140118000	Enhancers	Dnd41	blood
29	chr7:140117000-140117600	Enhancers	Primary hematopoietic stem cells	blood
30	chr7:140117000-140117600	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr7:140117000-140117800	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr7:140117000-140117800	Enhancers	Thymus	Thymus
33	chr7:140117200-140117600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr7:140117200-140117600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr7:140117200-140117800	Enhancers	Primary T cells fromperipheralblood	blood
36	chr7:140117200-140117800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:140117200-140117800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr7:140117400-140117600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr7:140117400-140117800	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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