Variant report

Variant	rs4243390
Chromosome Location	chr2:178468008-178468009
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10170667	0.87[CEU][hapmap];0.84[JPT][hapmap]
rs10201153	0.86[JPT][hapmap]
rs10497500	0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10497501	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10497503	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs10803909	0.81[EUR][1000 genomes]
rs10930798	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10930799	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10930800	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10930801	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11684320	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11689550	0.95[EUR][1000 genomes]
rs12463893	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12469386	0.89[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs12471741	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12612857	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12615367	0.86[JPT][hapmap]
rs12616093	0.86[JPT][hapmap]
rs12616443	0.81[EUR][1000 genomes]
rs12618139	0.81[JPT][hapmap]
rs12622298	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12991272	0.89[EUR][1000 genomes]
rs13000048	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs13004955	0.89[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs13013752	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13020788	0.89[CEU][hapmap];0.85[YRI][hapmap]
rs13027299	0.89[EUR][1000 genomes]
rs13034886	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs1348848	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs1348849	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs1348850	1.00[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1374437	0.89[CEU][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs1405713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1453370	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs1545364	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1548067	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16865328	0.86[JPT][hapmap]
rs16865331	0.86[JPT][hapmap]
rs1975543	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2060929	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs2084233	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs2121430	0.89[CEU][hapmap];0.86[CHB][hapmap];0.80[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs2166554	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2166558	0.89[CEU][hapmap]
rs2364854	0.94[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes]
rs3213945	0.86[JPT][hapmap]
rs3902850	0.89[CEU][hapmap]
rs3927978	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4243388	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs4341974	0.81[EUR][1000 genomes]
rs4528793	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4893822	0.89[CEU][hapmap]
rs4893823	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs4893825	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs4893950	0.89[CEU][hapmap];0.80[JPT][hapmap]
rs4893957	0.89[CEU][hapmap]
rs4893959	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs4893961	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4893962	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes]
rs4893965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4893966	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4893969	0.89[CEU][hapmap];0.84[YRI][hapmap]
rs4893972	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs6705405	0.81[ASW][hapmap];0.81[YRI][hapmap]
rs6710575	0.89[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs6734528	0.81[ASW][hapmap];0.89[CEU][hapmap];0.85[YRI][hapmap]
rs6734683	0.80[YRI][hapmap]
rs6736390	0.89[CEU][hapmap]
rs6742951	0.89[CEU][hapmap];0.81[JPT][hapmap]
rs6761593	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7559521	0.86[EUR][1000 genomes]
rs7565022	0.81[EUR][1000 genomes]
rs7587604	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7604673	0.89[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs7606235	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs8941	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs952746	0.89[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4243390	TTC30A	cis	Lymphoblastoid	GTEx
rs4243390	DKFZp451M2119	Cis_1M	lymphoblastoid	RTeQTL
rs4243390	TTC30B	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178462000-178468600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr2:178462800-178469000	Weak transcription	Small Intestine	intestine
3	chr2:178462800-178475600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:178462800-178482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:178463200-178471200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:178463200-178471200	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr2:178463600-178468600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:178463800-178475400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:178464200-178468600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr2:178464200-178469200	Weak transcription	Brain Anterior Caudate	brain
11	chr2:178464200-178471200	Weak transcription	HUVEC	blood vessel
12	chr2:178464200-178482600	Weak transcription	Psoas Muscle	Psoas
13	chr2:178464200-178482600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr2:178464400-178469000	Weak transcription	Brain Angular Gyrus	brain
15	chr2:178464400-178469000	Weak transcription	Left Ventricle	heart
16	chr2:178464600-178468200	Weak transcription	Adipose Nuclei	Adipose
17	chr2:178464600-178482400	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:178465600-178469400	Enhancers	Fetal Muscle Leg	muscle
19	chr2:178466000-178468800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr2:178466800-178468400	Enhancers	Fetal Stomach	stomach
21	chr2:178467000-178468600	Enhancers	Fetal Intestine Small	intestine
22	chr2:178467000-178469200	Enhancers	Fetal Intestine Large	intestine
23	chr2:178467400-178468200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:178467400-178468200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:178467400-178469000	Enhancers	Fetal Brain Female	brain
26	chr2:178467600-178468400	Enhancers	Fetal Brain Male	brain
27	chr2:178467600-178468400	Flanking Active TSS	Fetal Lung	lung
28	chr2:178467600-178469000	Enhancers	Ovary	ovary
29	chr2:178467600-178469200	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr2:178467600-178469400	Enhancers	Liver	Liver
31	chr2:178467800-178468400	Enhancers	Rectal Smooth Muscle	rectum
32	chr2:178467800-178468600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:178468000-178468200	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr2:178468000-178468600	Active TSS	Fetal Kidney	kidney
35	chr2:178468000-178469000	Enhancers	HepG2	liver

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