Variant report

Variant	rs4682357
Chromosome Location	chr3:111814717-111814718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111813838..111815744-chr3:111818709..111820600,2	K562	blood:
2	chr3:111804970..111806559-chr3:111814043..111816179,2	MCF-7	breast:
3	chr3:111813403..111815465-chr3:112280077..112281630,2	K562	blood:

Variant related genes	Relation type
ENSG00000144848	Chromatin interaction
ENSG00000114529	Chromatin interaction
ENSG00000138459	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10934145	0.92[CEU][hapmap]
rs10934162	0.80[CEU][hapmap]
rs11707558	0.92[CEU][hapmap]
rs11824	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11922559	0.92[CEU][hapmap]
rs12488760	0.92[CEU][hapmap]
rs12634769	0.92[CEU][hapmap]
rs13066495	0.89[CEU][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13074229	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13081485	0.84[CEU][hapmap]
rs13081935	0.85[CEU][hapmap]
rs13082509	0.85[CEU][hapmap]
rs13087086	0.85[CEU][hapmap]
rs13091454	0.88[CEU][hapmap]
rs13100724	0.85[CEU][hapmap]
rs2120095	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs340163	0.85[CEU][hapmap]
rs340165	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs340172	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3856723	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4234412	0.92[CEU][hapmap]
rs4234413	0.92[CEU][hapmap]
rs4276157	0.81[CEU][hapmap]
rs4282033	0.92[CEU][hapmap]
rs4392388	0.92[CEU][hapmap]
rs4401342	0.92[CEU][hapmap]
rs4505669	0.92[CEU][hapmap]
rs4560270	0.92[CEU][hapmap]
rs4572740	0.85[CEU][hapmap]
rs4585166	0.85[CEU][hapmap]
rs4611789	0.81[CEU][hapmap]
rs4632517	0.84[CEU][hapmap];0.81[TSI][hapmap]
rs4682097	0.91[CEU][hapmap]
rs4682355	0.94[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4682380	0.92[CEU][hapmap]
rs6773916	0.96[CEU][hapmap]
rs6781344	0.92[CEU][hapmap]
rs6798551	0.92[CEU][hapmap]
rs729641	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs746026	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs746027	0.91[EUR][1000 genomes]
rs7613061	0.92[CEU][hapmap]
rs7616261	0.92[CEU][hapmap]
rs7624367	0.92[CEU][hapmap]
rs7638520	0.92[CEU][hapmap]
rs923745	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9758396	0.92[CEU][hapmap]
rs9809384	0.92[CEU][hapmap]
rs9809404	0.92[CEU][hapmap]
rs9822786	0.92[CEU][hapmap]
rs9823421	0.92[CEU][hapmap]
rs9826043	0.92[CEU][hapmap]
rs9847574	0.91[CEU][hapmap]
rs9860819	0.92[CEU][hapmap]
rs9863061	0.88[CEU][hapmap]
rs9878213	0.92[CEU][hapmap]
rs9879184	0.92[CEU][hapmap]

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	esv2755927	chr3:111794310-111834310	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4682357	GCET2	cis	parietal	SCAN
rs4682357	KIAA1407	cis	parietal	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111806000-111821600	Weak transcription	Lung	lung
2	chr3:111806800-111816400	Weak transcription	Aorta	Aorta
3	chr3:111807000-111816200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:111810200-111815600	Weak transcription	HUVEC	blood vessel
5	chr3:111810400-111852000	Weak transcription	Esophagus	oesophagus
6	chr3:111812000-111814800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr3:111812000-111816000	Weak transcription	NHLF	lung
8	chr3:111812000-111816200	Weak transcription	GM12878-XiMat	blood
9	chr3:111812000-111825000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:111812000-111844000	Weak transcription	Colonic Mucosa	Colon
11	chr3:111812000-111845600	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:111812200-111815000	Weak transcription	Fetal Intestine Large	intestine
13	chr3:111812200-111815400	Weak transcription	HMEC	breast
14	chr3:111812200-111815800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr3:111812200-111816000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:111812200-111816400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:111812200-111820200	Weak transcription	Gastric	stomach
18	chr3:111812200-111820200	Weak transcription	Thymus	Thymus
19	chr3:111812200-111828000	Weak transcription	Left Ventricle	heart
20	chr3:111812200-111853000	Weak transcription	Right Ventricle	heart
21	chr3:111812400-111814800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:111812400-111815000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:111812400-111816000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:111812400-111816200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:111812400-111816200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:111812400-111816200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr3:111812400-111816200	Weak transcription	HSMM	muscle
28	chr3:111812400-111816600	Weak transcription	HSMMtube	muscle
29	chr3:111812400-111820400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr3:111812400-111820600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr3:111812400-111820800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:111812400-111821400	Weak transcription	Primary B cells from cord blood	blood
33	chr3:111812400-111822000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:111812400-111824800	Weak transcription	Primary T cells from cord blood	blood
35	chr3:111812400-111832000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:111812400-111835800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:111812600-111814800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:111812600-111816000	Weak transcription	Osteobl	bone
39	chr3:111812600-111821800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:111812600-111828000	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr3:111812600-111840200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:111813200-111815000	Weak transcription	Fetal Intestine Small	intestine
43	chr3:111813600-111815200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:111813800-111815200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr3:111814000-111814800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:111814000-111815000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:111814000-111815400	Genic enhancers	NH-A	brain
48	chr3:111814000-111817400	Enhancers	Placenta Amnion	Placenta Amnion
49	chr3:111814200-111814800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr3:111814200-111815000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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