Variant report

Variant	rs2486398
Chromosome Location	chr6:149318799-149318800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149304480..149307013-chr6:149318224..149319916,2	K562	blood:
2	chr11:51570628..51572150-chr6:149317397..149318917,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZC3H12D-13	chr6:149317093-149318982	ucscGeneNc_uc003qmh_1

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs2486390	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486392	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2486395	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2486397	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486400	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2486402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2486403	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2486404	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2486414	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2486415	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2486416	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2500525	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2500528	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2500530	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2500533	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2500535	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2500543	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2500545	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2500548	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6899672	1.00[CEU][hapmap]
rs9390651	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[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	nsv1032690	chr6:149206106-149398712	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv3380330	chr6:149318395-149318946	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149286800-149320600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr6:149292800-149321200	Weak transcription	Aorta	Aorta
3	chr6:149294000-149320400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:149294200-149319400	Weak transcription	HSMMtube	muscle
5	chr6:149300000-149319800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr6:149305400-149381400	Weak transcription	Gastric	stomach
7	chr6:149306200-149319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:149308000-149319600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:149308200-149320600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:149308400-149320400	Weak transcription	Right Ventricle	heart
11	chr6:149310200-149319600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:149310200-149335200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:149311000-149319400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:149311000-149321000	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr6:149311000-149321200	Weak transcription	Pancreas	Pancrea
16	chr6:149311000-149335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:149312600-149321000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:149314400-149319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:149314400-149321200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr6:149314800-149327400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr6:149315000-149319000	Weak transcription	Ovary	ovary
22	chr6:149315000-149319800	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:149315000-149320800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:149315000-149322200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:149316400-149320400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:149317000-149321800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr6:149317200-149319000	Weak transcription	Lung	lung
28	chr6:149317200-149319800	Weak transcription	Right Atrium	heart
29	chr6:149317200-149320600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr6:149317200-149320800	Weak transcription	Fetal Stomach	stomach
31	chr6:149317200-149321200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:149317200-149321200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr6:149317200-149321200	Weak transcription	Esophagus	oesophagus
34	chr6:149317200-149321400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr6:149317200-149321800	Enhancers	Osteobl	bone
36	chr6:149317600-149318800	Enhancers	NHDF-Ad	bronchial
37	chr6:149317600-149320600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:149317600-149321600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:149317600-149321800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr6:149317600-149321800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:149317600-149322000	Enhancers	HSMM	muscle
42	chr6:149317800-149320000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr6:149317800-149322200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr6:149318000-149319000	Weak transcription	NH-A	brain
45	chr6:149318000-149319200	Weak transcription	NHLF	lung
46	chr6:149318000-149320600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr6:149318000-149320800	Weak transcription	Primary B cells from cord blood	blood
48	chr6:149318200-149319400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:149318400-149322400	Enhancers	Dnd41	blood
50	chr6:149318600-149319000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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