Variant report

Variant	rs346500
Chromosome Location	chr4:86853558-86853559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10006487	1.00[JPT][hapmap]
rs10009525	0.84[JPT][hapmap]
rs189395	0.82[EUR][1000 genomes]
rs189396	0.83[EUR][1000 genomes]
rs2043647	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2136782	0.83[EUR][1000 genomes]
rs2164538	0.90[MEX][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2575681	0.81[EUR][1000 genomes]
rs2575682	0.81[EUR][1000 genomes]
rs2589505	0.81[EUR][1000 genomes]
rs2665869	0.90[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2665876	0.89[MEX][hapmap];0.85[MKK][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2869407	0.90[JPT][hapmap]
rs346469	0.90[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs346470	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs346473	0.90[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs346476	0.82[EUR][1000 genomes]
rs346477	0.82[EUR][1000 genomes]
rs346482	0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs346486	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs346487	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs346489	0.83[EUR][1000 genomes]
rs346490	0.83[EUR][1000 genomes]
rs346491	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs346493	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs346494	0.83[EUR][1000 genomes]
rs346495	0.83[EUR][1000 genomes]
rs346496	0.83[EUR][1000 genomes]
rs346497	1.00[JPT][hapmap]
rs346499	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs346501	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62305513	0.89[ASN][1000 genomes]
rs62305514	0.91[ASN][1000 genomes]
rs62305518	0.81[EUR][1000 genomes]
rs6531881	1.00[JPT][hapmap]
rs6820395	1.00[JPT][hapmap]
rs7670778	1.00[JPT][hapmap]
rs7696763	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv879519	chr4:86786204-86871282	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv879520	chr4:86829529-86918232	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs346500	FAM13A	cis	cerebellum	SCAN
rs346500	THAP9	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86844400-86853800	Weak transcription	Gastric	stomach
2	chr4:86848600-86856000	Weak transcription	Primary B cells from cord blood	blood
3	chr4:86850000-86853800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:86850400-86854400	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr4:86850800-86854000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:86850800-86854200	Active TSS	Fetal Kidney	kidney
7	chr4:86851200-86853800	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:86851200-86863200	Weak transcription	Psoas Muscle	Psoas
9	chr4:86851400-86853600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:86851400-86853600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:86851400-86853600	Weak transcription	Aorta	Aorta
12	chr4:86851400-86853600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr4:86851400-86853600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:86851400-86853600	Enhancers	HUVEC	blood vessel
15	chr4:86851400-86853800	Weak transcription	Lung	lung
16	chr4:86851400-86854400	Weak transcription	Spleen	Spleen
17	chr4:86851400-86861600	Weak transcription	Primary B cells from peripheral blood	blood
18	chr4:86851400-86865800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:86851400-86874600	Weak transcription	HSMMtube	muscle
20	chr4:86851600-86853600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:86851600-86853600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:86851600-86853600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr4:86851600-86853600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:86851600-86853600	Weak transcription	Fetal Brain Female	brain
25	chr4:86851600-86853600	Weak transcription	Pancreas	Pancrea
26	chr4:86851600-86853600	Weak transcription	Right Atrium	heart
27	chr4:86851600-86853800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:86851600-86853800	Weak transcription	Primary T cells from cord blood	blood
29	chr4:86851600-86853800	Weak transcription	Brain Angular Gyrus	brain
30	chr4:86851600-86853800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:86851600-86853800	Weak transcription	Placenta	Placenta
32	chr4:86851600-86853800	Enhancers	Dnd41	blood
33	chr4:86851600-86854000	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr4:86851600-86854000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:86851600-86854600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:86851600-86858200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr4:86851600-86870000	Weak transcription	HSMM	muscle
38	chr4:86851600-86874800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:86851800-86853600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr4:86851800-86853600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr4:86851800-86853600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr4:86851800-86853600	Weak transcription	Brain Cingulate Gyrus	brain
43	chr4:86851800-86853600	Weak transcription	Brain Germinal Matrix	brain
44	chr4:86851800-86853600	Weak transcription	Brain Hippocampus Middle	brain
45	chr4:86851800-86853600	Weak transcription	Fetal Intestine Large	intestine
46	chr4:86851800-86853600	Weak transcription	Fetal Intestine Small	intestine
47	chr4:86851800-86853600	Weak transcription	Fetal Stomach	stomach
48	chr4:86851800-86853600	Weak transcription	NHDF-Ad	bronchial
49	chr4:86851800-86854200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr4:86851800-86854200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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