Variant report

Variant	rs2645117
Chromosome Location	chr6:37954153-37954154
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	chr6:37919246..37922240-chr6:37953708..37956298,2	K562	blood:
2	chr6:37954058..37955830-chr6:37961204..37963273,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10456458	0.81[CHB][hapmap]
rs10485029	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[CHB][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs1074234	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10947707	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10947713	0.84[CEU][hapmap];0.89[CHB][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes]
rs1187421	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs12190570	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12194275	0.81[CHB][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap]
rs12194618	0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap]
rs12200258	0.89[CHB][hapmap]
rs12204352	0.88[CHB][hapmap]
rs12206414	0.81[CHB][hapmap]
rs12211248	0.89[CHB][hapmap]
rs12211981	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs12213835	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs13196716	0.81[CHB][hapmap]
rs13210701	0.89[CHB][hapmap]
rs16890344	0.93[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap]
rs171831	0.81[AFR][1000 genomes]
rs1967149	0.81[AMR][1000 genomes]
rs2055206	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2295791	0.81[CHB][hapmap];0.88[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs259679	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs259686	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs259689	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs259690	0.89[CHB][hapmap]
rs259691	0.89[CHB][hapmap]
rs259695	0.83[AFR][1000 genomes]
rs259713	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs259718	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2645102	0.88[CHB][hapmap]
rs2645107	0.89[CHB][hapmap]
rs2645113	0.90[AFR][1000 genomes]
rs2645116	0.89[CHB][hapmap]
rs2645120	0.91[AFR][1000 genomes]
rs2645124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2645127	0.95[AFR][1000 genomes]
rs2645131	0.80[CEU][hapmap];0.84[CHB][hapmap]
rs2645134	0.89[CHB][hapmap]
rs2645137	0.85[AFR][1000 genomes]
rs2842517	0.89[CHB][hapmap];1.00[CHD][hapmap]
rs2842527	1.00[ASW][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.96[LWK][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs2842529	0.90[AFR][1000 genomes]
rs34592529	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35806631	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35925070	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4714117	0.81[CHB][hapmap]
rs4714120	0.81[CHB][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs56098839	0.92[AFR][1000 genomes]
rs6458041	0.81[CHB][hapmap]
rs7747130	0.89[CHB][hapmap]
rs9394460	0.93[ASW][hapmap];0.87[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018711	chr6:37813397-37981590	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv602956	chr6:37909084-37986489	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv2761037	chr6:37930659-37966762	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2645117	KCNK17	cis	parietal	SCAN
rs2645117	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37922800-37957600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:37922800-37958600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:37926800-37955000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:37942800-37956800	Weak transcription	Aorta	Aorta
5	chr6:37943000-37955800	Weak transcription	Fetal Heart	heart
6	chr6:37946800-37955800	Weak transcription	Primary B cells from cord blood	blood
7	chr6:37948000-37954400	Weak transcription	A549	lung
8	chr6:37948000-37955400	Weak transcription	Left Ventricle	heart
9	chr6:37948000-37955400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:37948000-37956800	Weak transcription	Pancreas	Pancrea
11	chr6:37948200-37955200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:37948200-37955600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr6:37948400-37954800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:37948400-37955400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:37948400-37957600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:37948400-37958600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:37948600-37957800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:37949200-37955400	Weak transcription	Fetal Kidney	kidney
19	chr6:37949200-37955400	Weak transcription	Right Ventricle	heart
20	chr6:37949400-37954400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr6:37949600-37955400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:37949800-37955400	Weak transcription	Adipose Nuclei	Adipose
23	chr6:37949800-37955400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:37949800-37956800	Weak transcription	Right Atrium	heart
25	chr6:37949800-37962000	Weak transcription	Small Intestine	intestine
26	chr6:37950000-37954800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr6:37950000-37955400	Weak transcription	Brain Hippocampus Middle	brain
28	chr6:37950000-37963600	Weak transcription	Spleen	Spleen
29	chr6:37950400-37954200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:37950400-37955400	Weak transcription	Brain Substantia Nigra	brain
31	chr6:37950400-37956000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:37950400-37957000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr6:37950400-37958800	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr6:37950600-37954800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr6:37950600-37955400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:37951800-37959800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr6:37952200-37961400	Enhancers	Liver	Liver
38	chr6:37952400-37954600	Weak transcription	NHEK	skin
39	chr6:37952400-37955400	Weak transcription	Fetal Stomach	stomach
40	chr6:37952600-37954200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:37952600-37954200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:37952600-37957800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:37952600-37958600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:37952800-37955400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr6:37952800-37955400	Weak transcription	Primary T cells from cord blood	blood
46	chr6:37953200-37954200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr6:37953200-37954400	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr6:37953200-37954400	Enhancers	Gastric	stomach
49	chr6:37953400-37955400	Weak transcription	Ovary	ovary
50	chr6:37953400-37955800	Enhancers	Primary T helper cells fromperipheralblood	blood

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