Variant report

Variant	rs6561644
Chromosome Location	chr13:52263502-52263503
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12856726	0.82[MEX][hapmap]
rs1885855	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1923874	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4456399	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4533167	0.81[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4943008	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4943014	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7320201	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7327107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7984225	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7988297	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7990679	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9285179	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9526792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535716	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9535720	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568642	0.87[MEX][hapmap]
rs992583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6561644	NCRNA00282	cis	parietal	SCAN
rs6561644	TNNI2	trans	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52234000-52277800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr13:52247200-52277400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr13:52247600-52300200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr13:52247600-52300200	Weak transcription	Fetal Lung	lung
5	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr13:52251200-52269600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr13:52254400-52270200	Weak transcription	Esophagus	oesophagus
8	chr13:52254400-52273200	Weak transcription	Pancreas	Pancrea
9	chr13:52254600-52293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:52255400-52263600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:52255400-52273200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:52255600-52273200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:52256400-52277800	Weak transcription	HSMMtube	muscle
15	chr13:52257200-52263600	Weak transcription	NH-A	brain
16	chr13:52258000-52273400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr13:52258000-52280400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr13:52258200-52263600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:52258600-52271600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:52258600-52273400	Weak transcription	NHEK	skin
21	chr13:52258800-52270600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr13:52259000-52263600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr13:52259200-52278000	Weak transcription	Primary T cells from cord blood	blood
24	chr13:52259400-52273200	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr13:52259400-52277800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr13:52260600-52263800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:52261000-52273800	Weak transcription	Primary B cells from cord blood	blood
28	chr13:52261400-52263600	Enhancers	Brain Anterior Caudate	brain
29	chr13:52261400-52264200	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr13:52261600-52263600	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr13:52261600-52264200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr13:52261600-52264200	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr13:52261600-52264200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:52261600-52264200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:52261800-52264000	Enhancers	Fetal Brain Female	brain
36	chr13:52262000-52263600	Enhancers	Brain Angular Gyrus	brain
37	chr13:52262000-52263600	Enhancers	Brain Cingulate Gyrus	brain
38	chr13:52262000-52264000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr13:52262000-52264000	Enhancers	iPS-20b Cell Line	embryonic stem cell
40	chr13:52262000-52264200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr13:52262000-52264200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:52262000-52264200	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr13:52262400-52263600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr13:52262800-52264200	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr13:52262800-52269400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr13:52263000-52264200	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr13:52263000-52264200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:52263200-52263800	Enhancers	H1 Cell Line	embryonic stem cell
49	chr13:52263200-52263800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:52263200-52264000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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