Variant report

Variant	rs2496173
Chromosome Location	chr6:13382290-13382291
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13379880..13381834-chr6:13381972..13383883,2	MCF-7	breast:
2	chr6:13379945..13382317-chr6:13389702..13392053,2	MCF-7	breast:
3	chr6:13355357..13357068-chr6:13380690..13383506,2	MCF-7	breast:
4	chr6:13381851..13383974-chr6:13486160..13487948,2	MCF-7	breast:
5	chr6:13379696..13382625-chr6:13383447..13385433,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145990	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000237786	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10807431	0.92[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10807432	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10948650	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12153966	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2439536	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2496139	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2496160	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2496161	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.87[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2496162	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28813108	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4711978	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs474159	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs476904	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs489396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs491278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492433	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs501987	1.00[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs510932	0.92[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs516003	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs517803	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs524118	1.00[CEU][hapmap];0.84[CHB][hapmap];0.92[EUR][1000 genomes]
rs531256	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs548119	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs552655	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs553671	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553948	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs560396	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs564174	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs570315	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs573109	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs575709	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579028	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7760579	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7770078	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs821276	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821277	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9357708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9367440	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription 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
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13355600-13383400	Weak transcription	A549	lung
2	chr6:13365800-13385400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:13366000-13382800	Weak transcription	Liver	Liver
4	chr6:13366000-13386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:13368000-13404600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:13368400-13386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:13376000-13383400	Weak transcription	Psoas Muscle	Psoas
8	chr6:13376800-13386600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:13376800-13395200	Weak transcription	NHEK	skin
10	chr6:13377800-13383400	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr6:13377800-13395600	Weak transcription	Aorta	Aorta
12	chr6:13378200-13382400	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:13378400-13382400	Enhancers	Stomach Mucosa	stomach
14	chr6:13378600-13382400	Enhancers	Sigmoid Colon	Sigmoid Colon
15	chr6:13378600-13383200	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr6:13378600-13383600	Enhancers	GM12878-XiMat	blood
17	chr6:13379200-13382800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:13379200-13386600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:13379400-13382400	Enhancers	Adipose Nuclei	Adipose
20	chr6:13379400-13383600	Weak transcription	Spleen	Spleen
21	chr6:13379800-13383200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr6:13380200-13383600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr6:13380200-13389400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:13380400-13382400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:13380400-13383400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr6:13380600-13382400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:13380800-13382400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:13381000-13383400	Weak transcription	Fetal Lung	lung
29	chr6:13381000-13385800	Enhancers	Primary B cells from peripheral blood	blood
30	chr6:13381200-13382400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr6:13381200-13382400	Enhancers	HMEC	breast
32	chr6:13381200-13383400	Weak transcription	Gastric	stomach
33	chr6:13381200-13383600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr6:13381200-13383600	Weak transcription	Fetal Kidney	kidney
35	chr6:13381200-13384000	Weak transcription	Right Ventricle	heart
36	chr6:13381400-13382400	Enhancers	Esophagus	oesophagus
37	chr6:13381400-13383200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr6:13381400-13383600	Weak transcription	Brain Angular Gyrus	brain
39	chr6:13381400-13383600	Weak transcription	HepG2	liver
40	chr6:13381600-13382400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:13381600-13383400	Weak transcription	Colon Smooth Muscle	Colon
42	chr6:13381800-13382400	Genic enhancers	Lung	lung
43	chr6:13381800-13383400	Weak transcription	Brain Anterior Caudate	brain
44	chr6:13381800-13383400	Weak transcription	Brain Substantia Nigra	brain
45	chr6:13381800-13383400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:13381800-13383600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr6:13381800-13383800	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr6:13381800-13384600	Enhancers	Primary B cells from cord blood	blood
49	chr6:13381800-13395400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr6:13382000-13383800	Weak transcription	Colonic Mucosa	Colon

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