Variant report

Variant	rs6736390
Chromosome Location	chr2:178480314-178480315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:178479419..178481320-chr2:178491408..178493665,2	K562	blood:
2	chr2:178255832..178259686-chr2:178477259..178480585,3	K562	blood:
3	chr2:178255150..178257645-chr2:178478947..178480585,3	K562	blood:
4	chr2:178406620..178408509-chr2:178480094..178481704,2	K562	blood:
5	chr2:178479040..178481545-chr2:178589525..178591056,2	K562	blood:

Variant related genes	Relation type
ENSG00000116044	Chromatin interaction
ENSG00000018510	Chromatin interaction
ENSG00000213963	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10170667	0.81[CEU][hapmap]
rs1047884	0.88[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10497501	0.89[CEU][hapmap]
rs11678875	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs12467363	0.80[ASN][1000 genomes]
rs12471621	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12611503	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12612481	0.95[JPT][hapmap]
rs12612857	0.89[CEU][hapmap]
rs12616259	0.94[JPT][hapmap]
rs12619074	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12624192	0.89[ASN][1000 genomes]
rs12990917	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997716	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13008833	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap]
rs13008857	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs13009207	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13020788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13027895	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13031008	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13034781	0.80[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs1348850	0.89[CEU][hapmap]
rs1358328	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs1405713	0.89[CEU][hapmap]
rs1405714	0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs1405717	0.80[ASN][1000 genomes]
rs1405718	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1527401	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530034	0.90[JPT][hapmap]
rs1544002	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs1548067	0.89[CEU][hapmap]
rs2222711	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2293471	0.83[YRI][hapmap]
rs2364854	0.82[CEU][hapmap]
rs3770005	1.00[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs3770007	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs3770008	0.95[JPT][hapmap]
rs3770009	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3770011	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs3770012	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs4144276	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs4337505	0.94[JPT][hapmap]
rs4470372	0.81[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap]
rs4528793	0.89[CEU][hapmap]
rs4893838	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4893962	0.89[CEU][hapmap]
rs4893965	0.89[CEU][hapmap]
rs4893968	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4893969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55792594	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6734528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7605609	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7605757	0.80[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs880897	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs880898	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs880899	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	esv2762964	chr2:178416394-178481818	Weak transcription Active TSS Flanking Active TSS Enhancers 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv3506731	chr2:178416851-178482200	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
5	esv3506732	chr2:178416851-178482200	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
6	esv3520312	chr2:178417102-178482200	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv3520313	chr2:178417102-178482200	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv583689	chr2:178468008-178509820	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	esv1815823	chr2:178479149-178489902	Active TSS Enhancers Weak transcription Flanking 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 miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6736390	TTC30A	cis	lymphoblastoid	seeQTL
rs6736390	TTC30B	cis	parietal	SCAN
rs6736390	TTC30A	cis	multi-tissue	Pritchard
rs6736390	TTC30A	cis	Lymphoblastoid	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178462800-178482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:178464200-178482600	Weak transcription	Psoas Muscle	Psoas
3	chr2:178464200-178482600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:178464600-178482400	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:178468400-178482800	Weak transcription	Fetal Brain Male	brain
6	chr2:178471800-178482600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:178472600-178481000	Weak transcription	Fetal Kidney	kidney
8	chr2:178476000-178481000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:178476400-178482800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:178476800-178482600	Weak transcription	HepG2	liver
11	chr2:178477400-178482600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:178477600-178482600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:178477800-178482400	Weak transcription	Brain Substantia Nigra	brain
14	chr2:178477800-178482800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:178477800-178482800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:178479600-178482600	Weak transcription	HSMM	muscle
17	chr2:178479800-178480800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:178479800-178481000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr2:178480000-178481000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:178480000-178482600	Weak transcription	K562	blood
21	chr2:178480000-178482800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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