Variant report

Variant	rs9430273
Chromosome Location	chr1:9624113-9624114
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9622636..9625065-chr1:9627468..9629261,2	K562	blood:
2	chr1:9614835..9616919-chr1:9622620..9624442,2	K562	blood:
3	chr1:9611445..9613626-chr1:9623378..9625185,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10864429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12022881	0.81[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12023288	1.00[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12037667	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs12040542	0.94[ASW][hapmap];0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12045459	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12045493	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12070568	0.98[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12084279	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28719694	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923984	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4073710	0.88[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs4074744	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MKK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4244632	0.80[JPT][hapmap]
rs4423053	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4926482	0.92[EUR][1000 genomes]
rs55655211	0.92[ASN][1000 genomes]
rs55687246	0.89[ASN][1000 genomes]
rs55780537	0.92[ASN][1000 genomes]
rs55986711	0.92[ASN][1000 genomes]
rs56026893	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56053581	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57272167	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58478478	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs60744607	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs61782983	0.82[EUR][1000 genomes]
rs6540961	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6540962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6675436	0.92[EUR][1000 genomes]
rs6698575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72646709	0.92[ASN][1000 genomes]
rs72646712	0.92[ASN][1000 genomes]
rs72646713	0.92[ASN][1000 genomes]
rs72646715	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72646718	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7411273	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7525099	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7544083	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9430152	1.00[CEU][hapmap];0.81[GIH][hapmap];0.92[TSI][hapmap];0.96[EUR][1000 genomes]
rs9430153	1.00[CEU][hapmap];0.82[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9430174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9430180	0.83[EUR][1000 genomes]
rs9430182	0.83[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[ASN][1000 genomes]
rs9430184	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs9430274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9430332	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][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	nsv931984	chr1:8879337-9694749	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	570 gene(s)	inside rSNPs	diseases
2	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
3	nsv1013224	chr1:9441040-9699768	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv464283	chr1:9495571-9677853	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv545363	chr1:9495571-9677853	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9430273	SDC1	trans	lymphoblastoid	seeQTL
rs9430273	NPPA	cis	cerebellum	SCAN
rs9430273	HNRNPCL1	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9616200-9648200	Weak transcription	Esophagus	oesophagus
2	chr1:9616400-9638400	Weak transcription	Pancreas	Pancrea
3	chr1:9616800-9636600	Weak transcription	Gastric	stomach
4	chr1:9617000-9640200	Weak transcription	Placenta	Placenta
5	chr1:9618400-9624200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:9618600-9633600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:9618600-9648200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:9619000-9630400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr1:9619000-9631800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:9619200-9635800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:9619200-9635800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr1:9619200-9635800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:9619200-9636000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:9619200-9636000	Weak transcription	Spleen	Spleen
15	chr1:9619200-9648400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:9619200-9648400	Weak transcription	Aorta	Aorta
17	chr1:9619200-9648400	Weak transcription	Right Atrium	heart
18	chr1:9619400-9629400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr1:9619400-9631000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:9619400-9631600	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr1:9619400-9631600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:9619400-9633600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:9619400-9636000	Weak transcription	Brain Substantia Nigra	brain
24	chr1:9619600-9629800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr1:9619600-9631800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:9619600-9636000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:9619800-9624800	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:9619800-9639400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:9620000-9630800	Weak transcription	GM12878-XiMat	blood
30	chr1:9620000-9631000	Weak transcription	Primary T cells from cord blood	blood
31	chr1:9620000-9631200	Weak transcription	Fetal Muscle Leg	muscle
32	chr1:9620000-9635000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr1:9620200-9648200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr1:9620200-9648400	Weak transcription	Psoas Muscle	Psoas
35	chr1:9620400-9628200	Weak transcription	Fetal Stomach	stomach
36	chr1:9621000-9628200	Strong transcription	Dnd41	blood
37	chr1:9621000-9629400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr1:9621400-9636200	Weak transcription	Lung	lung
39	chr1:9621600-9631800	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr1:9621600-9648400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:9621800-9627400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:9621800-9627600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:9621800-9636200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr1:9621800-9637400	Weak transcription	Colonic Mucosa	Colon
45	chr1:9622000-9624200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:9622000-9625000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:9622000-9627600	Weak transcription	Fetal Heart	heart
48	chr1:9622000-9631600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr1:9622000-9631800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:9622000-9633400	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links