Variant report

Variant	rs916553
Chromosome Location	chr9:118160709-118160710
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10124142	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10124377	0.85[EUR][1000 genomes]
rs10739439	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10739440	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10739441	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10759774	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10759775	0.82[EUR][1000 genomes]
rs10759776	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10759777	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10759778	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10759779	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10817755	0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];0.80[YRI][hapmap]
rs10817762	0.82[CHB][hapmap]
rs10817763	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10817765	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10817768	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10817769	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982733	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982735	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982738	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10982741	0.82[EUR][1000 genomes]
rs1156578	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12552121	0.83[EUR][1000 genomes]
rs12686630	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1335141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1632833	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1632836	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1632839	0.84[EUR][1000 genomes]
rs1632840	0.84[EUR][1000 genomes]
rs1632845	0.83[EUR][1000 genomes]
rs1989766	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2020265	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2020279	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2078713	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2269700	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2418337	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2418341	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3983324	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3983325	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4978636	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4979525	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6478160	1.00[ASW][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[LWK][hapmap];1.00[YRI][hapmap]
rs7022390	0.81[EUR][1000 genomes]
rs7850103	1.00[ASW][hapmap];0.93[CHB][hapmap];0.80[YRI][hapmap]
rs7872215	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7872813	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9409143	0.80[YRI][hapmap]
rs9409144	0.80[YRI][hapmap]
rs9409145	0.87[CHB][hapmap];0.90[JPT][hapmap];0.80[YRI][hapmap]
rs9409146	0.87[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1042957	chr9:118153824-118313540	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2761245	chr9:118157164-118171298	Weak transcription Enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
5	nsv519995	chr9:118157729-118163797	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs916553	SLC31A1	cis	cerebellum	SCAN
rs916553	DNAJC25	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118154600-118161800	Weak transcription	Fetal Kidney	kidney
2	chr9:118157400-118162200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:118158800-118162600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:118158800-118163200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:118159000-118161400	Weak transcription	Right Atrium	heart
6	chr9:118159000-118161600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:118159000-118170600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:118159200-118161200	Weak transcription	Osteobl	bone
9	chr9:118159200-118161400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:118159200-118163000	Weak transcription	Fetal Muscle Leg	muscle
11	chr9:118159200-118163200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:118159200-118163200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:118159200-118163200	Weak transcription	NH-A	brain
14	chr9:118159200-118163800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:118160000-118164200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:118160400-118161000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr9:118160400-118161400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:118160400-118161800	Enhancers	Fetal Lung	lung
19	chr9:118160400-118164600	Enhancers	NHDF-Ad	bronchial
20	chr9:118160400-118173600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr9:118160600-118160800	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:118160600-118161400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:118160600-118161600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr9:118160600-118161600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr9:118160600-118161800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:118160600-118161800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:118160600-118162000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr9:118160600-118162200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:118160600-118163200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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