Variant report

Variant	rs10013042
Chromosome Location	chr4:120244482-120244483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10003567	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10006259	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10006525	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10006706	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10006877	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10013032	0.91[CEU][hapmap]
rs10017335	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10019674	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs10030660	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs10031033	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs10031483	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1011054	0.85[CHB][hapmap]
rs10518300	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs10518328	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs10518329	0.84[JPT][hapmap]
rs11098499	0.81[CHB][hapmap]
rs11098501	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11098530	0.81[CEU][hapmap]
rs11724758	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11726229	0.86[CHB][hapmap]
rs11729521	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs11732686	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11734241	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs11935596	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs11944880	0.81[CHB][hapmap]
rs12502423	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12507565	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12507964	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs12508504	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12510138	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12511640	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12513083	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12711071	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13113112	0.81[CHB][hapmap]
rs13129661	0.82[CHB][hapmap]
rs13134665	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs13149407	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs13435802	0.85[CHB][hapmap]
rs1383532	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1480931	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs1511017	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1511018	0.85[CHB][hapmap]
rs1511019	0.85[CHB][hapmap]
rs1511025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1546502	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap]
rs1546503	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1546505	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs17006190	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs1980025	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1980026	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2127821	0.83[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap]
rs2203039	0.90[CEU][hapmap]
rs2291185	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2389803	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2389809	0.81[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2892848	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs3733519	0.80[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap]
rs3733520	0.81[CEU][hapmap]
rs3733524	0.80[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap]
rs3749591	0.85[CHB][hapmap]
rs3775841	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs3775843	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs3775844	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs3775845	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6534130	0.86[CEU][hapmap]
rs6834796	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs6837898	0.85[CHB][hapmap]
rs6848389	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs6849171	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6849561	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs6849889	0.81[CHB][hapmap]
rs714899	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs7659194	0.86[CHB][hapmap]
rs7659501	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7665125	0.85[JPT][hapmap]
rs7672594	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7681544	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs7687843	0.81[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs7692994	0.83[JPT][hapmap]
rs7699064	0.80[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap]
rs878372	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs907205	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9991959	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9998585	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs9999724	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916641	chr4:119780023-120777320	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1012868	chr4:120014630-120464880	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv537232	chr4:120014630-120464880	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv428769	chr4:120205572-120363323	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv879840	chr4:120227419-120257417	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv2525765	chr4:120243529-120245168	Weak transcription Flanking Active TSS Active TSS Enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
7	esv3346833	chr4:120243754-120245852	Active TSS Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
8	nsv879841	chr4:120244085-120388406	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv879842	chr4:120244085-120424087	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv2018154	chr4:120244361-120245100	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
11	esv8767	chr4:120244404-120245164	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
12	esv3466094	chr4:120244454-120245001	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	esv3517491	chr4:120244459-120245048	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
14	esv3517489	chr4:120244463-120245007	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10013042	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	uninvolved skin	skin_eQTL
rs10013042	FLJ14186///LOC284701///LOC441124///LOC728624	Cis_1M	lymphoblastoid	RTeQTL
rs10013042	LOC645513	Cis_1M	lymphoblastoid	RTeQTL
rs10013042	LOC284701///FLJ14186///LOC441124///LOC641693///LOC642788///LOC653056	cis	lesional skin	skin_eQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120222000-120251000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr4:120222200-120244600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:120235600-120251000	Weak transcription	Left Ventricle	heart
4	chr4:120243600-120245200	Enhancers	Fetal Intestine Large	intestine
5	chr4:120244000-120245400	Enhancers	Fetal Intestine Small	intestine
6	chr4:120244400-120244800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr4:120244400-120249800	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links