Variant report

Variant	rs2731825
Chromosome Location	chr5:94886644-94886645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:94885448..94888187-chr5:94888844..94890737,5	K562	blood:
2	chr5:94869385..94872836-chr5:94884055..94887302,3	K562	blood:
3	chr5:94775142..94778090-chr5:94885546..94887301,2	K562	blood:
4	chr5:94885887..94888055-chr5:94890822..94893309,3	K562	blood:

Variant related genes	Relation type
ENSG00000198677	Chromatin interaction
ENSG00000225165	Chromatin interaction
ENSG00000164291	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10053324	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10076499	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1183640	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1541798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1981952	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2245588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2255165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2545841	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2548652	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2560257	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2560260	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560261	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2731826	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731833	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2881976	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6556870	0.84[ASN][1000 genomes]
rs73777211	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9314148	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2731825	TTC37	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94811000-94889400	Weak transcription	Stomach Mucosa	stomach
2	chr5:94827200-94889600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:94847400-94890000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:94849200-94890000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:94853800-94890000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:94864400-94889400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:94865200-94889400	Weak transcription	Esophagus	oesophagus
8	chr5:94865200-94890000	Weak transcription	Aorta	Aorta
9	chr5:94869400-94889000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:94870200-94889000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:94876200-94888800	Strong transcription	NHLF	lung
12	chr5:94877600-94889600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr5:94878400-94889400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:94879600-94889600	Weak transcription	Fetal Intestine Small	intestine
15	chr5:94879800-94886800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:94880000-94887600	Weak transcription	Small Intestine	intestine
17	chr5:94881000-94889600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:94881400-94889400	Weak transcription	Brain Substantia Nigra	brain
19	chr5:94881400-94889600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr5:94881600-94887200	Weak transcription	Fetal Heart	heart
21	chr5:94881600-94889200	Weak transcription	Fetal Brain Male	brain
22	chr5:94881600-94889600	Weak transcription	Thymus	Thymus
23	chr5:94881800-94887600	Weak transcription	NHEK	skin
24	chr5:94881800-94888200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr5:94881800-94889400	Weak transcription	Colonic Mucosa	Colon
26	chr5:94881800-94889400	Weak transcription	Spleen	Spleen
27	chr5:94882000-94888200	Weak transcription	Brain Germinal Matrix	brain
28	chr5:94882200-94888600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr5:94882400-94887200	Weak transcription	Psoas Muscle	Psoas
30	chr5:94882400-94889400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr5:94882400-94889400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:94882400-94889400	Weak transcription	Lung	lung
33	chr5:94882400-94889400	Weak transcription	Pancreas	Pancrea
34	chr5:94882400-94889400	Weak transcription	Right Ventricle	heart
35	chr5:94882400-94889600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:94882400-94889600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:94882400-94889600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr5:94882400-94889600	Weak transcription	Fetal Stomach	stomach
39	chr5:94882800-94887200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr5:94883000-94887000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:94883000-94887000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:94883000-94887200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:94883000-94887200	Weak transcription	Primary T cells from cord blood	blood
44	chr5:94883000-94887200	Weak transcription	Brain Angular Gyrus	brain
45	chr5:94883000-94889200	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:94883000-94889400	Weak transcription	Gastric	stomach
47	chr5:94883000-94889400	Weak transcription	K562	blood
48	chr5:94883000-94889600	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:94883000-94889600	Weak transcription	Left Ventricle	heart
50	chr5:94883000-94889600	Weak transcription	HSMMtube	muscle

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