Variant report

Variant	rs9869698
Chromosome Location	chr3:48580539-48580540
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48579149..48580932-chr3:48582283..48584303,2	K562	blood:
2	chr3:48580179..48583037-chr3:48585118..48587364,2	K562	blood:

Variant related genes	Relation type
ENSG00000114268	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1003649	0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes]
rs10049154	0.82[ASN][1000 genomes]
rs10470687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11706983	0.83[GIH][hapmap]
rs11708786	0.83[GIH][hapmap]
rs11719291	0.83[GIH][hapmap]
rs12107252	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs12107418	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13060933	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13062576	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs13063312	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13064619	0.82[ASN][1000 genomes]
rs13070798	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13091944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13094578	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs13100178	0.86[ASN][1000 genomes]
rs13319635	0.94[ASN][1000 genomes]
rs13319651	0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13324142	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13434258	0.83[GIH][hapmap]
rs17080289	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs2006871	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276850	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276852	0.80[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2286652	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2302295	1.00[JPT][hapmap]
rs2310996	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2854394	0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs2854395	0.88[ASN][1000 genomes]
rs28563843	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581474	0.86[ASN][1000 genomes]
rs28881595	0.81[ASN][1000 genomes]
rs35064573	0.83[GIH][hapmap]
rs35343040	0.80[ASN][1000 genomes]
rs35562294	0.92[ASN][1000 genomes]
rs3755819	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap]
rs3821875	1.00[JPT][hapmap]
rs3821876	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs3969942	0.95[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs4075082	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6442126	0.86[CHB][hapmap]
rs6442127	0.85[ASN][1000 genomes]
rs6765317	0.80[ASN][1000 genomes]
rs6773261	1.00[JPT][hapmap]
rs6781283	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6785845	0.82[ASN][1000 genomes]
rs6792156	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs6792525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806059	0.87[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];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6809981	0.82[ASN][1000 genomes]
rs740787	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7428949	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7434077	0.89[CHB][hapmap];0.90[CHD][hapmap];0.86[ASN][1000 genomes]
rs7434107	0.86[ASN][1000 genomes]
rs7620853	1.00[JPT][hapmap]
rs7623614	0.86[ASN][1000 genomes]
rs7631574	0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs7640031	0.86[ASN][1000 genomes]
rs7644771	0.86[ASN][1000 genomes]
rs9810549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811318	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9812200	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9814951	0.85[GIH][hapmap]
rs9816942	0.86[ASN][1000 genomes]
rs9821797	1.00[JPT][hapmap]
rs9822677	0.82[ASN][1000 genomes]
rs9830581	0.90[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9835827	0.82[ASN][1000 genomes]
rs9835902	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];0.85[ASN][1000 genomes]
rs9836462	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9837687	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9841602	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9843316	0.90[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9848824	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849280	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850102	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9851743	0.86[ASN][1000 genomes]
rs9851771	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.86[ASN][1000 genomes]
rs9864729	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871180	1.00[CEU][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871608	0.86[ASN][1000 genomes]
rs9873726	1.00[JPT][hapmap]
rs9875911	1.00[GIH][hapmap]
rs9878950	0.87[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.94[ASN][1000 genomes]
rs9881877	0.93[ASW][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9882549	0.83[GIH][hapmap]
rs9882962	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48555200-48582200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:48556200-48586800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr3:48556400-48586400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:48559600-48586400	Weak transcription	Primary B cells from cord blood	blood
6	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:48565800-48583600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:48568800-48586000	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:48570400-48580600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
11	chr3:48571000-48581800	Strong transcription	Fetal Intestine Small	intestine
12	chr3:48571400-48580600	Weak transcription	Left Ventricle	heart
13	chr3:48572200-48583800	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:48572600-48581800	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr3:48573400-48580600	Weak transcription	Adipose Nuclei	Adipose
16	chr3:48573400-48584400	Weak transcription	Fetal Kidney	kidney
17	chr3:48573600-48580600	Weak transcription	HSMM	muscle
18	chr3:48573600-48583600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:48573600-48589600	Weak transcription	Fetal Lung	lung
20	chr3:48573600-48592600	Weak transcription	NHDF-Ad	bronchial
21	chr3:48573600-48593400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:48574000-48583400	Weak transcription	Aorta	Aorta
23	chr3:48574000-48583400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:48574200-48586000	Weak transcription	Primary T cells from cord blood	blood
25	chr3:48574400-48583400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:48574400-48583400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr3:48574400-48591400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:48574800-48580600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:48574800-48583600	Weak transcription	NH-A	brain
30	chr3:48574800-48591200	Weak transcription	Dnd41	blood
31	chr3:48576000-48594000	Weak transcription	Small Intestine	intestine
32	chr3:48576200-48583600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr3:48576400-48583400	Weak transcription	Brain Angular Gyrus	brain
34	chr3:48576400-48583400	Weak transcription	A549	lung
35	chr3:48576400-48590200	Weak transcription	Colonic Mucosa	Colon
36	chr3:48576400-48591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:48576600-48583200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:48576600-48583600	Weak transcription	Osteobl	bone
39	chr3:48576800-48583600	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:48577000-48582800	Weak transcription	NHLF	lung
41	chr3:48577000-48583600	Weak transcription	Esophagus	oesophagus
42	chr3:48577200-48580600	Weak transcription	Spleen	Spleen
43	chr3:48577200-48583400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:48577200-48583600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:48577200-48583600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:48577200-48583600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:48577600-48580600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:48577600-48581000	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:48577600-48583400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr3:48577600-48583400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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