Variant report

Variant	rs2500545
Chromosome Location	chr6:149333388-149333389
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149011180..149013646-chr6:149332105..149333709,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2486390	0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2486392	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2486395	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2486396	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2486397	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2486398	0.90[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2486402	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[MEX][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2486403	0.90[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2486404	0.85[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2486413	0.88[ASN][1000 genomes]
rs2486414	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2486415	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2486416	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2500525	0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2500528	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2500530	0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2500533	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2500535	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2500543	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2500548	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390651	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2500545	KCTD14	trans	lymphoblastoid	seeQTL

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149305400-149381400	Weak transcription	Gastric	stomach
2	chr6:149310200-149335200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:149311000-149335200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:149320200-149335400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:149320200-149344800	Weak transcription	Left Ventricle	heart
6	chr6:149321600-149336000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr6:149321600-149340600	Weak transcription	Aorta	Aorta
8	chr6:149321800-149335000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:149321800-149340200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:149321800-149349800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:149322600-149334400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:149323000-149334400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:149323000-149334600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr6:149323000-149335600	Weak transcription	Fetal Lung	lung
15	chr6:149323000-149342600	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr6:149323600-149335600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:149324600-149334600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:149327200-149334200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr6:149327200-149334600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr6:149327200-149334800	Weak transcription	Fetal Stomach	stomach
21	chr6:149327200-149335200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr6:149327200-149340200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr6:149327200-149340600	Weak transcription	Primary B cells from cord blood	blood
24	chr6:149327200-149353000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr6:149327400-149334200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:149327400-149334800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:149327600-149335000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr6:149327600-149335800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:149327600-149342200	Weak transcription	Dnd41	blood
30	chr6:149328000-149335200	Weak transcription	Esophagus	oesophagus
31	chr6:149328600-149335200	Weak transcription	Fetal Muscle Leg	muscle
32	chr6:149329400-149340600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:149329800-149340200	Weak transcription	Ovary	ovary
34	chr6:149331800-149334800	Weak transcription	Fetal Heart	heart
35	chr6:149332400-149335200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:149332600-149333800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:149332600-149334400	Enhancers	HSMMtube	muscle
38	chr6:149332600-149336200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:149332600-149337800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr6:149332800-149333400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr6:149332800-149333400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:149332800-149333800	Enhancers	HSMM	muscle
43	chr6:149332800-149333800	Enhancers	NH-A	brain
44	chr6:149333000-149333400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:149333000-149333400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr6:149333000-149333400	Active TSS	A549	lung
47	chr6:149333000-149333400	Flanking Active TSS	Osteobl	bone
48	chr6:149333000-149333600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr6:149333000-149333800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr6:149333000-149333800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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