Variant report

Variant	rs6798412
Chromosome Location	chr3:43025986-43025987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 88 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10470680	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11129987	0.82[EUR][1000 genomes]
rs11129988	0.82[EUR][1000 genomes]
rs12629332	1.00[CHB][hapmap]
rs1392319	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1403525	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17074894	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238972	1.00[ASN][1000 genomes]
rs1816227	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28378297	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28601753	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655956	1.00[ASN][1000 genomes]
rs28673478	1.00[ASN][1000 genomes]
rs3915020	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4404423	1.00[CHB][hapmap]
rs489117	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs526511	0.83[EUR][1000 genomes]
rs530842	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs534284	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs542394	0.84[EUR][1000 genomes]
rs545023	0.84[EUR][1000 genomes]
rs551658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604393	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs60616619	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61004728	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs615462	0.82[EUR][1000 genomes]
rs617014	1.00[ASN][1000 genomes]
rs619660	0.82[EUR][1000 genomes]
rs62248962	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249006	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249007	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249008	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249009	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249011	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249013	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249014	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249015	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62249016	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62249584	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs638602	0.83[EUR][1000 genomes]
rs649682	0.83[EUR][1000 genomes]
rs651899	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6763762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773223	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775999	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782601	1.00[MEX][hapmap]
rs678310	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6798520	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs680967	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs681341	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[MEX][hapmap];1.00[ASN][1000 genomes]
rs73075297	1.00[ASN][1000 genomes]
rs73075301	1.00[ASN][1000 genomes]
rs73077208	1.00[ASN][1000 genomes]
rs73077214	1.00[ASN][1000 genomes]
rs73077238	1.00[ASN][1000 genomes]
rs73087348	1.00[ASN][1000 genomes]
rs735320	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[MEX][hapmap];1.00[ASN][1000 genomes]
rs73832423	1.00[ASN][1000 genomes]
rs73832424	1.00[ASN][1000 genomes]
rs7617715	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7625959	0.94[CEU][hapmap];0.90[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs7641452	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644923	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs834183	0.83[EUR][1000 genomes]
rs834579	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs834584	1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs834699	0.83[EUR][1000 genomes]
rs9311330	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9311331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9808932	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815609	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9816391	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9824700	1.00[ASN][1000 genomes]
rs9828785	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]
rs9832875	0.89[ASW][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9833284	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837761	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840349	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9852930	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9858270	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862469	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9865715	1.00[CHB][hapmap]
rs9870478	0.80[CEU][hapmap];1.00[CHB][hapmap];0.81[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6798412	HIGD1A	cis	cerebellum	SCAN
rs6798412	KIF15	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43021400-43030200	Weak transcription	Aorta	Aorta
2	chr3:43022000-43033000	Weak transcription	Pancreas	Pancrea
3	chr3:43022000-43037000	Weak transcription	Right Atrium	heart
4	chr3:43022200-43027600	Weak transcription	Placenta	Placenta
5	chr3:43022200-43032800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:43022400-43026800	Weak transcription	Brain Substantia Nigra	brain
7	chr3:43022800-43027600	Weak transcription	Fetal Intestine Small	intestine
8	chr3:43022800-43030000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:43023000-43037800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:43023200-43029600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:43023400-43026400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:43023400-43029600	Weak transcription	Liver	Liver
13	chr3:43024000-43026600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:43024000-43027400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:43024200-43026600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:43024200-43026800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:43024200-43027200	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr3:43024200-43027400	Enhancers	H1 Cell Line	embryonic stem cell
19	chr3:43024400-43027000	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr3:43024800-43027000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr3:43025000-43026600	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:43025400-43026600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:43025600-43026400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr3:43025600-43026600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr3:43025800-43026000	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:43025800-43026000	Enhancers	Ovary	ovary
27	chr3:43025800-43026200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr3:43025800-43026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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