Variant report

Variant	rs4970941
Chromosome Location	chr1:151068546-151068547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10749659	0.90[ASN][1000 genomes]
rs10788797	0.89[CHB][hapmap]
rs10788798	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs10788800	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10888404	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10888405	0.82[EUR][1000 genomes]
rs11204772	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11204777	0.86[JPT][hapmap]
rs11204779	0.97[ASN][1000 genomes]
rs11204780	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs11204782	0.85[JPT][hapmap]
rs11807526	0.86[JPT][hapmap]
rs12039522	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12087892	0.86[JPT][hapmap]
rs12093562	0.83[ASN][1000 genomes]
rs12134957	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12569193	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.82[EUR][1000 genomes]
rs1524773	0.85[JPT][hapmap]
rs15740	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap]
rs2067606	0.86[JPT][hapmap]
rs2091219	0.87[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap]
rs2140709	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs2864700	1.00[CHB][hapmap];0.94[CHD][hapmap]
rs2902810	0.88[CHD][hapmap]
rs3738481	0.85[JPT][hapmap]
rs3806386	0.88[CHD][hapmap]
rs4357530	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.95[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs4360524	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4512652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs4970936	0.88[ASN][1000 genomes]
rs4970940	0.81[ASN][1000 genomes]
rs4970991	0.82[CHB][hapmap]
rs4970993	0.86[JPT][hapmap]
rs4970998	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4971005	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4971007	0.88[CHD][hapmap];0.86[JPT][hapmap]
rs4971008	0.82[CHD][hapmap];0.86[JPT][hapmap]
rs61819219	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6587552	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs6587553	0.88[CHD][hapmap]
rs6656450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6674970	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap]
rs6676190	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691701	0.82[CHB][hapmap]
rs6697617	0.97[ASN][1000 genomes]
rs6704195	0.83[ASN][1000 genomes]
rs7414477	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7522608	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7523731	0.86[JPT][hapmap]
rs7536234	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7554936	0.96[CEU][hapmap];0.86[JPT][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872421	chr1:151055670-151098077	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4970941	LYSMD1	cis	parietal	SCAN
rs4970941	PRPF3	cis	cerebellum	SCAN
rs4970941	BNIPL	cis	lung	GTEx
rs4970941	CDC42SE1	cis	lymphoblastoid	seeQTL
rs4970941	PRPF3	cis	parietal	SCAN
rs4970941	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs4970941	GABPB2	cis	cerebellum	SCAN
rs4970941	ZNF687	cis	cerebellum	SCAN
rs4970941	PEX11B	cis	parietal	SCAN
rs4970941	CDC42SE1	cis	parietal	SCAN
rs4970941	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
2	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
3	chr1:151044200-151069800	Weak transcription	HSMM	muscle
4	chr1:151044200-151070800	Weak transcription	Fetal Lung	lung
5	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
6	chr1:151044400-151079000	Weak transcription	Left Ventricle	heart
7	chr1:151044400-151079600	Weak transcription	Lung	lung
8	chr1:151044400-151090200	Weak transcription	Gastric	stomach
9	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
10	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
11	chr1:151044600-151069600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr1:151044600-151069800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:151044600-151069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:151044600-151070000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:151044600-151076000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:151044600-151080400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:151044600-151080600	Weak transcription	Brain Anterior Caudate	brain
18	chr1:151044600-151081000	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:151044800-151069800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:151044800-151070400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:151044800-151079600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr1:151044800-151080200	Weak transcription	Fetal Brain Female	brain
23	chr1:151044800-151089400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:151045000-151070400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr1:151045000-151079400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr1:151045000-151080000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:151045000-151080400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:151045200-151081000	Weak transcription	Placenta	Placenta
30	chr1:151045800-151070400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr1:151046000-151069800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr1:151047200-151090400	Weak transcription	Dnd41	blood
33	chr1:151047400-151069800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:151047400-151090400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:151047600-151069200	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr1:151047600-151069800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr1:151047600-151075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:151047800-151079600	Weak transcription	Fetal Muscle Leg	muscle
39	chr1:151047800-151089200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:151052200-151103000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:151054400-151070400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:151056200-151079600	Weak transcription	Primary B cells from cord blood	blood
43	chr1:151057800-151075200	Weak transcription	Psoas Muscle	Psoas
44	chr1:151059200-151069600	Weak transcription	Hela-S3	cervix
45	chr1:151060600-151090200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:151061400-151079200	Weak transcription	Osteobl	bone
47	chr1:151061800-151070600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:151061800-151090400	Weak transcription	Fetal Kidney	kidney
49	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:151062000-151079400	Weak transcription	Primary neutrophils fromperipheralblood	blood

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