Variant report

Variant	rs4267734
Chromosome Location	chr4:15586225-15586226
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11726647	0.86[JPT][hapmap]
rs13106528	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13114491	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13122812	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13127507	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13131119	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13131285	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13138894	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13141724	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13144428	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468735	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1468736	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16892135	1.00[JPT][hapmap]
rs16892143	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16892156	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17476670	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17476831	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1786	0.87[ASW][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap];0.80[YRI][hapmap]
rs2041672	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2041673	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3182730	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34155734	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34427409	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34599140	0.85[ASN][1000 genomes]
rs34831330	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34924677	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35151159	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35196224	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35258636	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35309200	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35461787	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3756247	0.86[JPT][hapmap]
rs41417147	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs4301111	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs4326008	1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4396986	0.87[ASW][hapmap];0.86[JPT][hapmap]
rs4423870	0.80[ASW][hapmap];0.86[JPT][hapmap];0.82[MKK][hapmap]
rs4549375	0.86[JPT][hapmap];0.80[YRI][hapmap]
rs4613560	0.85[ASN][1000 genomes]
rs6414764	0.86[JPT][hapmap];0.81[YRI][hapmap]
rs6449150	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66472670	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67047740	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67089836	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67222859	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67224550	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6815254	0.87[ASW][hapmap];0.86[JPT][hapmap]
rs6824422	0.86[JPT][hapmap]
rs6825051	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6825815	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6826058	0.87[ASW][hapmap];0.86[JPT][hapmap];0.89[MKK][hapmap];0.81[YRI][hapmap]
rs6834359	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6835038	1.00[JPT][hapmap]
rs6839654	0.87[ASW][hapmap];0.86[JPT][hapmap];0.81[YRI][hapmap]
rs6844141	1.00[JPT][hapmap]
rs6848779	0.81[YRI][hapmap]
rs6852735	0.85[JPT][hapmap]
rs7699180	0.80[ASN][1000 genomes]
rs9994518	0.86[MKK][hapmap];0.84[YRI][hapmap]

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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4267734	FAM200B	cis	parietal	SCAN
rs4267734	C1QTNF7	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
2	chr4:15537400-15621000	Weak transcription	Hela-S3	cervix
3	chr4:15546000-15589600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr4:15550000-15617800	Weak transcription	Thymus	Thymus
5	chr4:15554600-15601400	Weak transcription	A549	lung
6	chr4:15555800-15589400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:15556000-15603200	Weak transcription	Fetal Thymus	thymus
8	chr4:15564000-15600600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr4:15564400-15603200	Weak transcription	HMEC	breast
10	chr4:15564600-15603600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:15565400-15612600	Weak transcription	Brain Substantia Nigra	brain
12	chr4:15565400-15621400	Weak transcription	Esophagus	oesophagus
13	chr4:15565600-15604200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr4:15565600-15611400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:15565800-15605000	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:15566200-15596800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr4:15568400-15655600	Weak transcription	Gastric	stomach
18	chr4:15568600-15589400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr4:15569600-15588600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:15569600-15596400	Weak transcription	NHDF-Ad	bronchial
21	chr4:15569600-15603600	Weak transcription	Spleen	Spleen
22	chr4:15569600-15604200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:15570200-15601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr4:15570600-15588200	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:15570600-15602000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:15570600-15602000	Weak transcription	Pancreas	Pancrea
27	chr4:15570800-15588800	Weak transcription	Psoas Muscle	Psoas
28	chr4:15570800-15589600	Weak transcription	Lung	lung
29	chr4:15571000-15597200	Weak transcription	Brain Hippocampus Middle	brain
30	chr4:15571200-15588000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr4:15571200-15588800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:15571400-15596000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:15572000-15593400	Weak transcription	Fetal Brain Male	brain
34	chr4:15572200-15586800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr4:15572200-15588200	Weak transcription	Adipose Nuclei	Adipose
36	chr4:15572200-15588600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:15572200-15591600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr4:15572200-15593600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:15572200-15595600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:15572200-15601200	Weak transcription	NHLF	lung
41	chr4:15572200-15601800	Weak transcription	Brain Angular Gyrus	brain
42	chr4:15572200-15601800	Weak transcription	NHEK	skin
43	chr4:15572200-15604000	Weak transcription	Primary T cells from cord blood	blood
44	chr4:15572200-15604200	Weak transcription	Duodenum Mucosa	Duodenum
45	chr4:15572400-15596200	Weak transcription	Ovary	ovary
46	chr4:15572800-15588800	Weak transcription	Fetal Brain Female	brain
47	chr4:15573000-15588400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr4:15573200-15603800	Weak transcription	Fetal Intestine Small	intestine
49	chr4:15574800-15593200	Weak transcription	Brain Germinal Matrix	brain
50	chr4:15575200-15618000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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