Variant report

Variant	rs4835469
Chromosome Location	chr4:148832250-148832251
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10001756	0.83[EUR][1000 genomes]
rs10003507	0.82[CEU][hapmap];0.84[JPT][hapmap];0.89[EUR][1000 genomes]
rs10004138	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs10004691	0.85[EUR][1000 genomes]
rs10004792	0.82[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10014593	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10014696	0.82[CEU][hapmap]
rs10015875	0.83[EUR][1000 genomes]
rs10018820	0.82[CEU][hapmap]
rs10025069	0.83[EUR][1000 genomes]
rs10026985	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10030358	0.82[CEU][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10049932	0.82[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11099671	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs11099672	0.82[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11734553	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11735412	0.82[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs11737346	0.80[MKK][hapmap]
rs12331562	0.82[CEU][hapmap]
rs12509618	0.82[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12513192	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs12643550	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13129325	0.82[CEU][hapmap]
rs13129809	0.87[ASW][hapmap];0.85[YRI][hapmap]
rs13151898	0.85[EUR][1000 genomes]
rs1369958	0.82[CEU][hapmap];0.83[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17024037	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs17613979	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs17614025	0.90[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17676080	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs187006	0.81[CHB][hapmap]
rs2043643	0.85[EUR][1000 genomes]
rs2043645	0.85[EUR][1000 genomes]
rs2118033	0.81[CHB][hapmap];0.85[MEX][hapmap]
rs2358181	0.81[CHB][hapmap]
rs2635256	0.81[CHB][hapmap]
rs2635266	0.81[CHB][hapmap]
rs2635268	0.81[CHB][hapmap]
rs28576385	0.83[EUR][1000 genomes]
rs28614116	0.85[EUR][1000 genomes]
rs2884400	0.87[EUR][1000 genomes]
rs34970355	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35243600	0.85[EUR][1000 genomes]
rs35899247	0.85[EUR][1000 genomes]
rs3893175	0.82[CEU][hapmap];0.86[EUR][1000 genomes]
rs3990920	0.82[CEU][hapmap];0.88[GIH][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4240341	0.82[CEU][hapmap];0.81[CHD][hapmap]
rs4491995	0.82[CEU][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4571312	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs4627844	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4835103	0.84[GIH][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs4835109	0.80[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4835110	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4835468	0.82[ASN][1000 genomes]
rs55650760	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55820558	0.85[EUR][1000 genomes]
rs62330732	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62330735	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62330737	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6535569	0.82[EUR][1000 genomes]
rs6811769	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6818371	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6840771	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6843392	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs6856273	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs7660508	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs7666127	0.82[CEU][hapmap]
rs7677632	0.85[EUR][1000 genomes]
rs7698670	0.84[EUR][1000 genomes]
rs893033	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs9991741	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs9994650	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs9995956	0.82[CEU][hapmap]
rs9997027	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1017904	chr4:148814133-148975348	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1024596	chr4:148830472-148886915	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4835469	C9orf93	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
2	chr4:148796800-148863200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr4:148796800-148866000	Weak transcription	Thymus	Thymus
4	chr4:148797000-148834200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:148797000-148835800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr4:148797400-148879600	Weak transcription	Gastric	stomach
7	chr4:148804600-148854400	Weak transcription	Psoas Muscle	Psoas
8	chr4:148820600-148833400	Weak transcription	Left Ventricle	heart
9	chr4:148820600-148861200	Weak transcription	Esophagus	oesophagus
10	chr4:148820800-148848800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:148823400-148836600	Weak transcription	Placenta	Placenta
12	chr4:148823600-148833400	Weak transcription	Fetal Stomach	stomach
13	chr4:148823600-148833800	Weak transcription	NHLF	lung
14	chr4:148823600-148834600	Weak transcription	Fetal Intestine Large	intestine
15	chr4:148824400-148842800	Weak transcription	Lung	lung
16	chr4:148824400-148854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:148824600-148854400	Weak transcription	Right Ventricle	heart
18	chr4:148824800-148833400	Weak transcription	Fetal Intestine Small	intestine
19	chr4:148825000-148834000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:148825000-148836200	Weak transcription	HMEC	breast
21	chr4:148825200-148834000	Weak transcription	NHDF-Ad	bronchial
22	chr4:148825200-148835400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr4:148825200-148839600	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr4:148825200-148847400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr4:148825200-148848400	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr4:148825400-148832400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr4:148825400-148834000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:148825400-148834000	Weak transcription	Osteobl	bone
29	chr4:148825400-148843400	Weak transcription	Fetal Heart	heart
30	chr4:148825400-148844200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:148825400-148846200	Weak transcription	Fetal Kidney	kidney
32	chr4:148825400-148861200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr4:148825400-148865800	Weak transcription	Fetal Lung	lung
34	chr4:148826600-148888200	Weak transcription	Fetal Thymus	thymus
35	chr4:148827200-148832800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:148827400-148861200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:148828400-148834200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr4:148828400-148836400	Strong transcription	Aorta	Aorta
39	chr4:148829000-148834600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:148829000-148836400	Weak transcription	Ovary	ovary
41	chr4:148829400-148836200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr4:148829400-148864200	Weak transcription	Primary T cells from cord blood	blood
43	chr4:148830000-148832600	Strong transcription	Fetal Muscle Trunk	muscle
44	chr4:148830000-148833400	Weak transcription	Stomach Smooth Muscle	stomach
45	chr4:148830200-148841200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr4:148830400-148833800	Weak transcription	HSMMtube	muscle
47	chr4:148830600-148833400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr4:148830600-148840200	Weak transcription	Spleen	Spleen
49	chr4:148830800-148832600	Strong transcription	GM12878-XiMat	blood
50	chr4:148830800-148834400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links