Variant report

Variant	rs1103996
Chromosome Location	chr6:110017595-110017596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1096137	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1096141	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11153196	0.95[CEU][hapmap]
rs12175588	0.95[CEU][hapmap]
rs12194431	0.95[CEU][hapmap]
rs12209401	0.80[EUR][1000 genomes]
rs1321208	0.89[CEU][hapmap]
rs1406955	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs1923057	0.84[EUR][1000 genomes]
rs2025149	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2145145	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs2884130	0.84[EUR][1000 genomes]
rs3799852	0.82[ASW][hapmap];0.95[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs3823234	0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4945838	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs4947005	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs4947007	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4947013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4947014	0.91[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4947020	0.82[EUR][1000 genomes]
rs62435962	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6899688	0.84[EUR][1000 genomes]
rs6899915	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6906729	0.94[CEU][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6912209	0.82[EUR][1000 genomes]
rs6921615	0.82[ASW][hapmap];0.95[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs6933962	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6936853	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6941211	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7757153	0.81[EUR][1000 genomes]
rs7757895	0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap]
rs7759120	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7763229	0.95[CEU][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs7764711	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs7770807	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7771150	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7772817	0.81[EUR][1000 genomes]
rs829810	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs829811	0.91[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs865503	0.95[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs866685	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9285400	0.84[EUR][1000 genomes]
rs9372223	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9374111	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs9374112	0.87[EUR][1000 genomes]
rs9384712	0.95[CEU][hapmap]
rs9384719	0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs9386819	0.95[CEU][hapmap]
rs9386822	0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs9386828	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs9386829	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs9398210	0.82[ASW][hapmap];0.95[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs9398212	0.87[EUR][1000 genomes]
rs9480980	0.95[CEU][hapmap]
rs9487132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9487161	0.82[CEU][hapmap]
rs9487181	0.87[EUR][1000 genomes]
rs9487211	0.81[EUR][1000 genomes]
rs9766863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]

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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv933105	chr6:109933270-110064342	ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv604485	chr6:109959269-110054486	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1103996	AKD1	cis	cerebellum	SCAN
rs1103996	RFPL4B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:110013000-110022400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:110013000-110023600	Weak transcription	Gastric	stomach
4	chr6:110013000-110024800	Weak transcription	Lung	lung
5	chr6:110013000-110025200	Weak transcription	Small Intestine	intestine
6	chr6:110013000-110027400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:110013000-110027400	Weak transcription	Spleen	Spleen
8	chr6:110013000-110057000	Weak transcription	Left Ventricle	heart
9	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
10	chr6:110013200-110020200	Weak transcription	Colonic Mucosa	Colon
11	chr6:110013200-110022200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr6:110013200-110022400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr6:110013200-110024200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:110013200-110026400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:110013200-110026600	Weak transcription	Ovary	ovary
16	chr6:110013200-110034000	Weak transcription	Fetal Stomach	stomach
17	chr6:110013200-110057000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr6:110013200-110057000	Weak transcription	Aorta	Aorta
19	chr6:110013400-110022200	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr6:110013400-110023200	Weak transcription	Fetal Intestine Large	intestine
21	chr6:110013400-110038600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr6:110013600-110018600	Weak transcription	Osteobl	bone
23	chr6:110013600-110022200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr6:110013600-110022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:110013600-110022600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr6:110013600-110056000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr6:110013600-110056800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr6:110013800-110018000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:110013800-110018600	Weak transcription	NHDF-Ad	bronchial
30	chr6:110013800-110026400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:110013800-110026600	Weak transcription	Brain Substantia Nigra	brain
32	chr6:110013800-110029600	Weak transcription	Fetal Lung	lung
33	chr6:110014000-110017600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:110014000-110027400	Weak transcription	Brain Angular Gyrus	brain
35	chr6:110014000-110034400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:110014200-110018000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:110014400-110018600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr6:110014400-110023600	Weak transcription	Thymus	Thymus
39	chr6:110014600-110017800	Weak transcription	Brain Germinal Matrix	brain
40	chr6:110014600-110018000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:110014600-110018600	Weak transcription	Adipose Nuclei	Adipose
42	chr6:110014600-110022400	Weak transcription	Psoas Muscle	Psoas
43	chr6:110014600-110026600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr6:110014800-110018800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr6:110014800-110023200	Weak transcription	Stomach Mucosa	stomach
46	chr6:110014800-110023600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr6:110014800-110023800	Weak transcription	Fetal Thymus	thymus
48	chr6:110014800-110026200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr6:110014800-110026400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:110014800-110026600	Weak transcription	Liver	Liver

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