Variant report

Variant	rs2496162
Chromosome Location	chr6:13361088-13361089
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13306050..13307672-chr6:13360364..13362318,2	K562	blood:
2	chr6:13357478..13359612-chr6:13359699..13362212,2	K562	blood:
3	chr6:13353670..13357830-chr6:13359815..13362315,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D7-2	chr6:13358067-13361194	NONHSAT107804

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10807431	0.93[CEU][hapmap]
rs10948650	0.87[EUR][1000 genomes]
rs1140251	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12153966	0.96[CEU][hapmap]
rs2439536	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2496139	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2496160	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2496161	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2496173	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4711978	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs476904	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs489396	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs491278	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs492433	0.86[EUR][1000 genomes]
rs501987	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs510932	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs516003	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs517803	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs524118	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs531256	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs548119	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs552655	0.85[EUR][1000 genomes]
rs553671	0.84[EUR][1000 genomes]
rs553948	0.89[EUR][1000 genomes]
rs560396	0.86[EUR][1000 genomes]
rs564174	0.85[EUR][1000 genomes]
rs570315	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs573109	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs575709	0.93[CEU][hapmap];0.84[EUR][1000 genomes]
rs579028	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7760579	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs7770078	0.92[CEU][hapmap]
rs821276	0.88[EUR][1000 genomes]
rs821277	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs9357708	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9367440	0.92[CEU][hapmap];0.88[EUR][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:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13350800-13364600	Weak transcription	Aorta	Aorta
2	chr6:13355400-13364000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:13355600-13383400	Weak transcription	A549	lung
4	chr6:13356000-13364400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:13356000-13364400	Weak transcription	Stomach Mucosa	stomach
6	chr6:13356200-13362800	Weak transcription	Liver	Liver
7	chr6:13356200-13362800	Weak transcription	Fetal Kidney	kidney
8	chr6:13356200-13362800	Weak transcription	Fetal Lung	lung
9	chr6:13356200-13364000	Weak transcription	Esophagus	oesophagus
10	chr6:13356200-13364400	Weak transcription	Pancreas	Pancrea
11	chr6:13356200-13364600	Weak transcription	Lung	lung
12	chr6:13356200-13364800	Weak transcription	Colonic Mucosa	Colon
13	chr6:13356200-13365000	Weak transcription	Gastric	stomach
14	chr6:13356200-13367600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr6:13356200-13371800	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:13356200-13372000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:13356200-13373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:13356200-13378200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:13356400-13361800	Enhancers	Primary B cells from peripheral blood	blood
20	chr6:13356400-13365000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:13356400-13368000	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:13357200-13364600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:13357400-13361600	Enhancers	Primary B cells from cord blood	blood
24	chr6:13358000-13364400	Weak transcription	Brain Germinal Matrix	brain
25	chr6:13358000-13364400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr6:13358000-13364600	Weak transcription	Primary T cells from cord blood	blood
27	chr6:13358000-13364600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:13358000-13364800	Weak transcription	Dnd41	blood
29	chr6:13358000-13371800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:13358200-13362800	Weak transcription	NHLF	lung
31	chr6:13358200-13364400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:13358200-13364600	Weak transcription	Thymus	Thymus
33	chr6:13358200-13367600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr6:13358200-13368200	Weak transcription	HMEC	breast
35	chr6:13358400-13361200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr6:13358400-13362400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:13358400-13367600	Weak transcription	NH-A	brain
38	chr6:13358600-13361200	Weak transcription	GM12878-XiMat	blood
39	chr6:13358600-13361400	Enhancers	Adipose Nuclei	Adipose
40	chr6:13358600-13361800	Enhancers	Right Ventricle	heart
41	chr6:13358800-13365000	Weak transcription	Fetal Muscle Leg	muscle
42	chr6:13358800-13365800	Strong transcription	Stomach Smooth Muscle	stomach
43	chr6:13358800-13367400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr6:13359000-13362800	Enhancers	Left Ventricle	heart
45	chr6:13359000-13364600	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:13359000-13367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr6:13359200-13363000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:13359200-13364600	Weak transcription	Brain Anterior Caudate	brain
49	chr6:13359200-13365000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr6:13359200-13367400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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