Variant report

Variant	rs9399481
Chromosome Location	chr6:144906833-144906834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:144905902..144906972-chr6:145534873..145536365,4	K562	blood:
2	chr6:144901193..144904643-chr6:144905764..144908311,3	K562	blood:
3	chr6:144906028..144907293-chr6:145349130..145350022,4	MCF-7	breast:
4	chr6:144906099..144907163-chr6:145349098..145349929,4	MCF-7	breast:
5	chr6:144906108..144907031-chr6:145535323..145536185,3	MCF-7	breast:
6	chr6:144906202..144908261-chr6:145458578..145460342,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152818	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12661566	1.00[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12663647	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12664494	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12664819	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534442	0.87[JPT][hapmap]
rs1534443	0.87[JPT][hapmap]
rs1534444	0.87[JPT][hapmap]
rs17073972	0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1918751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918752	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997252	0.96[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2091486	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2293536	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3811100	0.96[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4076068	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4896728	1.00[CHB][hapmap];0.81[JPT][hapmap];0.98[ASN][1000 genomes]
rs6906465	0.87[JPT][hapmap]
rs9321980	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9373415	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs9376823	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9376824	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9376826	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9376828	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9386070	0.88[ASN][1000 genomes]
rs9386071	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9386072	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9386073	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9390170	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9390172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390174	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9390175	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9390176	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9390178	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9390184	0.83[JPT][hapmap]
rs9399480	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403563	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9403564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9403567	0.96[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9403572	0.83[JPT][hapmap]
rs9497009	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015228	chr6:144780458-144989321	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv538462	chr6:144780458-144989321	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144881800-144937800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:144885800-144943400	Weak transcription	Ovary	ovary
3	chr6:144898600-144912800	Weak transcription	Gastric	stomach
4	chr6:144899600-144909000	Weak transcription	Aorta	Aorta
5	chr6:144899600-144913800	Weak transcription	Lung	lung
6	chr6:144899600-144931800	Weak transcription	Esophagus	oesophagus
7	chr6:144899800-144914400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:144899800-144914400	Weak transcription	Fetal Intestine Small	intestine
9	chr6:144899800-144917400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr6:144900000-144915400	Weak transcription	Pancreas	Pancrea
11	chr6:144902400-144908400	Weak transcription	HUVEC	blood vessel
12	chr6:144904200-144907400	Active TSS	Brain Anterior Caudate	brain
13	chr6:144904400-144907000	Active TSS	Fetal Thymus	thymus
14	chr6:144904400-144931600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:144904400-144931800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:144904600-144910400	Weak transcription	Right Ventricle	heart
17	chr6:144904600-144913000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:144904600-144913600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:144904600-144913800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:144904600-144914400	Weak transcription	HSMM	muscle
21	chr6:144904600-144915800	Weak transcription	Psoas Muscle	Psoas
22	chr6:144904600-144915800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr6:144904600-144916400	Weak transcription	Fetal Stomach	stomach
24	chr6:144904600-144921600	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:144904600-144923600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr6:144904600-144939800	Weak transcription	HSMMtube	muscle
27	chr6:144904800-144907200	Weak transcription	Fetal Heart	heart
28	chr6:144904800-144908200	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr6:144904800-144908400	Weak transcription	Fetal Intestine Large	intestine
30	chr6:144904800-144908800	Weak transcription	HepG2	liver
31	chr6:144904800-144909000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:144904800-144911000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:144904800-144913400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:144904800-144914200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:144904800-144914200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr6:144904800-144914200	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr6:144904800-144914600	Weak transcription	Spleen	Spleen
38	chr6:144904800-144915800	Weak transcription	NH-A	brain
39	chr6:144904800-144921200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:144904800-144929000	Weak transcription	Left Ventricle	heart
41	chr6:144904800-144935400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr6:144905000-144907000	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr6:144905000-144907800	Weak transcription	Primary B cells from peripheral blood	blood
44	chr6:144905000-144908000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr6:144905000-144908600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:144905000-144908600	Weak transcription	Adipose Nuclei	Adipose
47	chr6:144905000-144908800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:144905000-144909000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:144905000-144909800	Weak transcription	Fetal Kidney	kidney
50	chr6:144905200-144912200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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