Variant report

Variant	rs10513468
Chromosome Location	chr3:154825259-154825260
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:154823311..154825797-chr3:154828920..154830559,2	K562	blood:

Variant related genes	Relation type
ENSG00000196549	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10513470	1.00[JPT][hapmap]
rs1370031	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[TSI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17384425	1.00[JPT][hapmap]
rs17442808	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3773884	1.00[JPT][hapmap]
rs3773889	1.00[JPT][hapmap]
rs4273335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4273336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56189742	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62279988	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62279989	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62279990	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6763852	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1000140	chr3:154336261-154905740	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv534289	chr3:154535584-154987166	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv532663	chr3:154561578-154960353	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10513468	RSRC1	cis	parietal	SCAN
rs10513468	DHX36	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:154800400-154826800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:154808200-154827200	Weak transcription	Fetal Intestine Large	intestine
3	chr3:154808800-154825400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:154815600-154827400	Weak transcription	Liver	Liver
5	chr3:154815800-154834000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:154818200-154827400	Genic enhancers	Dnd41	blood
7	chr3:154818800-154827000	Weak transcription	Fetal Thymus	thymus
8	chr3:154819400-154844400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:154819600-154827000	Weak transcription	Fetal Intestine Small	intestine
10	chr3:154819600-154828400	Weak transcription	Fetal Kidney	kidney
11	chr3:154819800-154825400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:154819800-154826400	Weak transcription	Thymus	Thymus
13	chr3:154820400-154825400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:154820600-154834800	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:154820600-154836600	Weak transcription	NHLF	lung
16	chr3:154820800-154826600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:154821200-154826600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:154821200-154829000	Weak transcription	HSMM	muscle
19	chr3:154821800-154825600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:154824200-154884400	Weak transcription	Psoas Muscle	Psoas
21	chr3:154824400-154825600	Weak transcription	NHDF-Ad	bronchial
22	chr3:154824400-154826600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:154824600-154825400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:154824600-154829000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:154824800-154827000	Weak transcription	Fetal Lung	lung
26	chr3:154825200-154825600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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