Variant report

Variant	rs17197663
Chromosome Location	chr13:38172867-38172868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr13:38172590-38173094	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr13:38172698-38173044	SK-N-SH	brain:	n/a	n/a
3	EP300	chr13:38172701-38173012	SK-N-SH_RA	brain:	n/a	n/a
4	POLR2A	chr13:38172730-38173026	SK-N-SH	brain:	n/a	n/a
5	TAF1	chr13:38172701-38173016	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr13:38172591-38173070	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr13:38172596-38173023	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr13:38172600-38173112	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr13:38172549-38173234	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr13:38172811-38172953	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr13:38172705-38173039	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr13:38172666-38172959	ProgFib	skin:	n/a	n/a
13	EP300	chr13:38172699-38173061	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
POSTN	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11147663	1.00[JPT][hapmap]
rs12583344	1.00[JPT][hapmap]
rs12585258	1.00[JPT][hapmap]
rs17056196	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197978	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17199299	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17199750	0.92[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17201866	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17257154	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17257328	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17257579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17258158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17258368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17261242	0.86[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1924295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924302	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1924303	1.00[JPT][hapmap]
rs1951895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829364	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41306668	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4512969	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4628831	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61532724	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6750	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73182620	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73182622	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73182624	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73182687	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73182690	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184525	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184528	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184530	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184531	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184532	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184534	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73184537	0.82[EUR][1000 genomes]
rs73186506	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73186523	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73186543	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs73186546	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7338811	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548007	1.00[JPT][hapmap]
rs9548010	0.89[JPT][hapmap]
rs9548011	1.00[JPT][hapmap]
rs9548017	1.00[JPT][hapmap]
rs9603242	1.00[JPT][hapmap]

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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1038850	chr13:37820489-38209571	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv34109	chr13:37843819-38276391	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1045716	chr13:37952062-38394595	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv832583	chr13:38030752-38202000	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17197663	KL	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38165800-38182400	Weak transcription	Placenta	Placenta
2	chr13:38168800-38173400	Active TSS	Fetal Muscle Trunk	muscle
3	chr13:38169200-38173000	Active TSS	NH-A	brain
4	chr13:38169400-38173600	Active TSS	NHLF	lung
5	chr13:38169800-38175600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:38169800-38175600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr13:38170400-38173400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:38170400-38173600	Active TSS	Fetal Stomach	stomach
9	chr13:38170600-38173600	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr13:38170600-38174200	Active TSS	Fetal Muscle Leg	muscle
11	chr13:38170800-38173000	Active TSS	Rectal Mucosa Donor 29	rectum
12	chr13:38170800-38173200	Active TSS	Right Atrium	heart
13	chr13:38171000-38173000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
14	chr13:38171000-38173200	Active TSS	Adipose Nuclei	Adipose
15	chr13:38171200-38173000	Active TSS	Duodenum Smooth Muscle	Duodenum
16	chr13:38171200-38173000	Active TSS	Fetal Intestine Large	intestine
17	chr13:38171200-38173200	Active TSS	Muscle Satellite Cultured Cells	--
18	chr13:38171200-38173400	Active TSS	Fetal Lung	lung
19	chr13:38171200-38173600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr13:38171200-38173600	Active TSS	Stomach Smooth Muscle	stomach
21	chr13:38171400-38173000	Active TSS	Colon Smooth Muscle	Colon
22	chr13:38171400-38173800	Active TSS	Osteobl	bone
23	chr13:38171600-38173000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr13:38171600-38173400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr13:38171600-38173800	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr13:38171800-38173200	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr13:38172000-38175400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr13:38172200-38175600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:38172600-38173000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr13:38172600-38173000	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr13:38172600-38173000	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr13:38172600-38173000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr13:38172600-38173000	Active TSS	Left Ventricle	heart
34	chr13:38172600-38173000	Flanking Active TSS	NHDF-Ad	bronchial
35	chr13:38172600-38173600	Enhancers	NHEK	skin
36	chr13:38172800-38173000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:38172800-38173000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr13:38172800-38173000	Flanking Active TSS	Fetal Kidney	kidney
39	chr13:38172800-38173000	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr13:38172800-38173200	Enhancers	H1 Cell Line	embryonic stem cell
41	chr13:38172800-38174200	Enhancers	HUVEC	blood vessel
42	chr13:38172800-38175600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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