Variant report

Variant	rs6830078
Chromosome Location	chr4:48790336-48790337
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:48783390..48785837-chr4:48789039..48791747,3	K562	blood:
2	chr4:48780486..48785837-chr4:48787089..48791393,6	K562	blood:
3	chr4:48784590..48786986-chr4:48788593..48791116,3	MCF-7	breast:
4	chr4:48782469..48785403-chr4:48787452..48790375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075539	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10003273	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10008265	0.85[EUR][1000 genomes]
rs10010571	0.83[ASN][1000 genomes]
rs11727343	0.81[EUR][1000 genomes]
rs11939889	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11943219	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12512637	0.83[EUR][1000 genomes]
rs12641022	0.83[EUR][1000 genomes]
rs13119414	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13141523	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13141838	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13142540	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1517674	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1554256	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1554258	0.85[EUR][1000 genomes]
rs1589107	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1702798	0.80[EUR][1000 genomes]
rs1712767	0.80[EUR][1000 genomes]
rs1980193	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2056201	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2176460	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2354314	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2572345	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2572350	0.81[EUR][1000 genomes]
rs2712156	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2712157	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2712158	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2712159	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28733443	0.80[EUR][1000 genomes]
rs2883562	0.83[EUR][1000 genomes]
rs4694906	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4695397	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4695400	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4695401	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57797824	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62309747	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6447655	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447660	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6814811	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6830848	0.83[EUR][1000 genomes]
rs6853588	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7657332	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7657698	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7660206	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7665209	0.83[EUR][1000 genomes]
rs7680280	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7681070	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7697522	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs955683	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9790336	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002674	chr4:48507608-49032909	Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537087	chr4:48507608-49032909	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
3	nsv1010923	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537088	chr4:48575156-49083089	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1013762	chr4:48580484-49032909	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv537089	chr4:48580484-49032909	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1793455	chr4:48686817-48859142	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1010381	chr4:48701525-49309842	Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1003718	chr4:48771947-49083089	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv916809	chr4:48784318-49083302	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv1011910	chr4:48784332-49154757	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6830078	OCIAD1	Cis_1M	lymphoblastoid	RTeQTL
rs6830078	SLC10A4	cis	lung	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48786600-48791200	Enhancers	Brain Cingulate Gyrus	brain
2	chr4:48788200-48791200	Enhancers	Brain Hippocampus Middle	brain
3	chr4:48789400-48790600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:48789600-48791800	Enhancers	Brain Substantia Nigra	brain
5	chr4:48789600-48801000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr4:48789800-48791800	Enhancers	Brain Anterior Caudate	brain
7	chr4:48790000-48791600	Enhancers	Brain Angular Gyrus	brain
8	chr4:48790200-48791000	Enhancers	Fetal Kidney	kidney
9	chr4:48790200-48794000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr4:48790200-48794400	Weak transcription	Brain Inferior Temporal Lobe	brain

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