Variant report

Variant	rs13243476
Chromosome Location	chr7:104435897-104435898
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:104427635..104430340-chr7:104433804..104436120,2	K562	blood:
2	chr7:104435065..104439363-chr7:104442614..104444965,4	K562	blood:
3	chr7:104435065..104437773-chr7:104442766..104444672,2	K562	blood:

Variant related genes	Relation type
ENSG00000226869	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10256308	0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs10270391	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12540437	0.92[CEU][hapmap]
rs12540497	0.82[JPT][hapmap]
rs12669981	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12671054	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12673938	0.92[CEU][hapmap]
rs12705276	0.92[CEU][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs12705277	0.86[JPT][hapmap]
rs12705278	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12705280	0.83[EUR][1000 genomes]
rs13230337	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13236549	0.86[JPT][hapmap]
rs13238018	0.92[CEU][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2465065	0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs34557807	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34680468	0.81[EUR][1000 genomes]
rs35708701	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36059846	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4400324	0.92[CEU][hapmap];0.86[JPT][hapmap];0.82[TSI][hapmap]
rs58902803	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61195574	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67577079	0.80[EUR][1000 genomes]
rs67775507	0.81[EUR][1000 genomes]
rs6964274	0.86[JPT][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429790	chr7:104314049-104488049	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv429792	chr7:104400049-104488049	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv5887	chr7:104401250-104491604	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030875	chr7:104409391-104472647	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1028479	chr7:104409391-104479087	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv528392	chr7:104411273-104466675	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv522743	chr7:104411273-104486707	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv831086	chr7:104422503-104596766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1019625	chr7:104429371-104461487	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13243476	DNAJC2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104430800-104436800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr7:104431800-104436000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr7:104433400-104439600	Weak transcription	Fetal Intestine Small	intestine
4	chr7:104434000-104436800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr7:104434000-104436800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:104434200-104437000	Enhancers	Brain Substantia Nigra	brain
7	chr7:104434200-104441200	Weak transcription	Fetal Intestine Large	intestine
8	chr7:104434400-104436200	Enhancers	Osteobl	bone
9	chr7:104434400-104437000	Enhancers	Brain Hippocampus Middle	brain
10	chr7:104434600-104436800	Enhancers	Brain Cingulate Gyrus	brain
11	chr7:104434600-104437200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr7:104435000-104436400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:104435000-104436600	Enhancers	Brain Germinal Matrix	brain
14	chr7:104435200-104437000	Enhancers	HUVEC	blood vessel
15	chr7:104435400-104436000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr7:104435600-104438600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:104435800-104436000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain

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