Variant report

Variant	rs7436583
Chromosome Location	chr4:110333106-110333107
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110331995..110333806-chr4:110335263..110337273,2	K562	blood:

Variant related genes	Relation type
ENSG00000247950	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs10000545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10002595	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10005355	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10016533	0.93[CEU][hapmap];1.00[MEX][hapmap]
rs10028250	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10155127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10516558	0.93[CEU][hapmap];0.92[GIH][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11098033	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11098035	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11929713	0.83[CEU][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11930655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11933172	0.81[CHD][hapmap]
rs11933971	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11934486	0.96[ASN][1000 genomes]
rs11935440	1.00[ASN][1000 genomes]
rs11935629	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs11938593	1.00[ASN][1000 genomes]
rs11941344	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11942140	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11942291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11942858	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11942928	1.00[ASN][1000 genomes]
rs11943384	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11943430	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11944375	1.00[ASN][1000 genomes]
rs11944427	1.00[ASN][1000 genomes]
rs11944659	0.96[ASN][1000 genomes]
rs12639832	0.96[ASN][1000 genomes]
rs12640049	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640161	0.96[ASN][1000 genomes]
rs12642304	0.90[ASN][1000 genomes]
rs12643055	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12643844	0.90[ASN][1000 genomes]
rs12644055	0.82[CHB][hapmap];1.00[ASN][1000 genomes]
rs12647695	1.00[ASN][1000 genomes]
rs12648138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12648965	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12650654	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12650873	1.00[ASN][1000 genomes]
rs13103034	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13110999	0.86[CEU][hapmap]
rs13122093	0.86[CEU][hapmap]
rs13123618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13125368	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13128124	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13128221	0.93[CEU][hapmap];0.89[EUR][1000 genomes]
rs13128445	0.85[MEX][hapmap]
rs13134239	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13138833	0.82[AMR][1000 genomes]
rs13140373	0.86[CEU][hapmap]
rs13141701	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13142698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13143825	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13145066	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1509314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1509315	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040410	1.00[ASN][1000 genomes]
rs17040436	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040439	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040461	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17040488	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17040510	0.80[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17585970	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs17619262	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs2346014	0.82[AMR][1000 genomes]
rs28521972	0.86[ASN][1000 genomes]
rs28681408	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34153531	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34224638	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34274964	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34377662	0.83[ASN][1000 genomes]
rs34441811	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34482781	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34505473	0.87[EUR][1000 genomes]
rs34636377	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34836476	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35110951	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35359830	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35473144	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35594044	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35762958	0.90[ASN][1000 genomes]
rs35791246	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35940980	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs36009064	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36115572	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3775962	0.90[ASN][1000 genomes]
rs60957336	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61004219	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61242473	0.88[ASN][1000 genomes]
rs61439452	0.98[ASN][1000 genomes]
rs61553525	1.00[ASN][1000 genomes]
rs6533426	0.82[AMR][1000 genomes]
rs6533428	0.90[ASN][1000 genomes]
rs6533429	1.00[ASN][1000 genomes]
rs6533434	1.00[MEX][hapmap]
rs66642182	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66667140	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67473696	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68041341	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6812469	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6815455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6817954	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6818911	0.86[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6823032	0.90[ASN][1000 genomes]
rs6825928	0.88[MEX][hapmap]
rs6827006	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6833753	0.88[ASN][1000 genomes]
rs6835683	0.86[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6837199	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6841198	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6845371	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6848452	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851517	1.00[ASN][1000 genomes]
rs6852037	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6856291	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6856446	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs71603033	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72896619	0.96[ASN][1000 genomes]
rs72896622	0.96[ASN][1000 genomes]
rs72896625	0.96[ASN][1000 genomes]
rs72896629	0.96[ASN][1000 genomes]
rs72896632	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73838809	0.90[ASN][1000 genomes]
rs7436745	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7440371	1.00[ASN][1000 genomes]
rs7440570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7675602	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679836	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7680296	0.88[EUR][1000 genomes]
rs7687245	1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs876464	0.82[AMR][1000 genomes]
rs9985632	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9985964	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9993228	0.82[AMR][1000 genomes]
rs9994676	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9994985	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9996432	0.82[AMR][1000 genomes]
rs9999570	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv1799708	chr4:110309234-110333106	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7436583	SEC24B	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110328800-110353600	Weak transcription	Brain Germinal Matrix	brain
2	chr4:110329800-110333400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:110329800-110334400	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr4:110330200-110334000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:110330400-110339600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr4:110330600-110333600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:110330800-110333400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr4:110330800-110335800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:110331600-110333800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:110332000-110334400	Enhancers	HSMMtube	muscle
11	chr4:110332200-110333200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr4:110332200-110333400	Weak transcription	HSMM	muscle
13	chr4:110332200-110335400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:110332400-110333800	Enhancers	Fetal Muscle Leg	muscle
15	chr4:110332400-110335600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr4:110332400-110340400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:110332600-110333200	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr4:110332600-110333400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr4:110332600-110333800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr4:110332600-110335200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:110332800-110334200	Enhancers	Fetal Heart	heart
22	chr4:110332800-110336000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr4:110333000-110333400	Enhancers	Fetal Stomach	stomach
24	chr4:110333000-110333600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr4:110333000-110333600	Enhancers	Brain Hippocampus Middle	brain
26	chr4:110333000-110333800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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