Variant report

Variant	rs6783218
Chromosome Location	chr3:43031952-43031953
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10212191	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs10510736	0.82[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs13080201	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17390473	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17455509	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17455760	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17469719	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs2001682	0.82[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap]
rs2062517	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs28435122	0.82[EUR][1000 genomes]
rs28548208	0.81[EUR][1000 genomes]
rs2948619	0.81[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs34100558	0.96[ASN][1000 genomes]
rs35110063	0.88[EUR][1000 genomes]
rs3953390	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs531888	0.89[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap]
rs532792	0.82[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs55701670	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55848724	0.87[ASN][1000 genomes]
rs56292257	0.82[ASN][1000 genomes]
rs62247060	0.82[EUR][1000 genomes]
rs62247061	0.83[EUR][1000 genomes]
rs62247062	0.83[EUR][1000 genomes]
rs6442134	0.85[EUR][1000 genomes]
rs644534	0.82[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap]
rs66603383	0.96[ASN][1000 genomes]
rs67186096	0.87[ASN][1000 genomes]
rs6764648	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[EUR][1000 genomes]
rs6792817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793871	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6794402	0.82[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs6806427	0.89[CEU][hapmap];0.87[CHB][hapmap];0.86[EUR][1000 genomes]
rs6807814	0.96[ASN][1000 genomes]
rs704918	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7616750	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7619227	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7624799	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7633590	0.89[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.85[EUR][1000 genomes]
rs7634125	0.93[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7637698	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7643433	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs834177	0.89[CEU][hapmap];0.87[CHB][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs872126	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs9311332	0.92[CEU][hapmap];0.93[CHB][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs9812262	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9821320	1.00[CEU][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs9848904	0.82[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap]
rs9858123	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9863179	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9872107	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874514	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv460523	chr3:43025986-43063406	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv590150	chr3:43025986-43063406	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv3390521	chr3:43030448-43032446	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv513044	chr3:43030479-43032100	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a
7	esv2496441	chr3:43030917-43032274	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6783218	PTH1R	cis	cerebellum	SCAN
rs6783218	KIF15	cis	parietal	SCAN
rs6783218	CCR9	cis	parietal	SCAN
rs6783218	HIGD1A	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43022000-43033000	Weak transcription	Pancreas	Pancrea
2	chr3:43022000-43037000	Weak transcription	Right Atrium	heart
3	chr3:43022200-43032800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:43023000-43037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:43026600-43032000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:43026600-43032400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:43026600-43032800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:43026800-43032400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr3:43027000-43033200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:43027200-43032800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:43027400-43032200	Weak transcription	Fetal Thymus	thymus
12	chr3:43029800-43033200	Weak transcription	Esophagus	oesophagus
13	chr3:43030000-43032400	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:43030200-43032000	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:43030400-43032200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:43030400-43032200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:43030400-43032400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:43030400-43032400	Weak transcription	Brain Angular Gyrus	brain
19	chr3:43030400-43032600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:43030400-43033000	Weak transcription	Ovary	ovary
21	chr3:43030400-43033600	Weak transcription	Adipose Nuclei	Adipose
22	chr3:43030600-43033000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:43030600-43033000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:43030800-43032200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:43030800-43032200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:43030800-43032200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:43030800-43032200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:43030800-43032400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:43030800-43032800	Weak transcription	Brain Substantia Nigra	brain
30	chr3:43030800-43037800	Weak transcription	Liver	Liver
31	chr3:43031000-43032000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:43031200-43034200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:43031600-43032800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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