Variant report

Variant	rs1563445
Chromosome Location	chr11:93246042-93246043
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	chr11:93220502..93222563-chr11:93243476..93246294,2	K562	blood:
2	chr11:93239199..93241218-chr11:93245473..93247114,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10466368	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11601056	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11604909	0.86[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs2243410	0.92[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2248020	1.00[CEU][hapmap];0.87[GIH][hapmap];0.83[TSI][hapmap];0.96[EUR][1000 genomes]
rs2248524	0.93[CEU][hapmap];0.93[EUR][1000 genomes]
rs2248531	0.93[EUR][1000 genomes]
rs2248655	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2263368	1.00[CHB][hapmap]
rs2605611	0.91[ASW][hapmap];0.86[CEU][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2605614	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2605615	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2605617	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2605620	0.93[EUR][1000 genomes]
rs2605622	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605623	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2605627	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2605628	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2605629	0.91[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2658766	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2658768	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2658769	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2658770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2658778	0.82[ASW][hapmap];0.83[TSI][hapmap]
rs2658779	0.82[ASW][hapmap];0.83[TSI][hapmap]
rs2658781	0.82[ASW][hapmap];0.83[TSI][hapmap]
rs2658791	0.80[EUR][1000 genomes]
rs2925355	0.82[ASW][hapmap]
rs7116173	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1563445	CHORDC1	cis	parietal	SCAN
rs1563445	MTNR1B	cis	parietal	SCAN
rs1563445	CCDC67	cis	Thyroid	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
2	chr11:93218600-93254400	Weak transcription	Hela-S3	cervix
3	chr11:93225600-93248800	Weak transcription	Fetal Muscle Leg	muscle
4	chr11:93226400-93257400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr11:93227200-93257600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr11:93228200-93248200	Weak transcription	Brain Hippocampus Middle	brain
7	chr11:93232800-93248800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr11:93233000-93248800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr11:93233000-93248800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:93233000-93257400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr11:93233400-93248600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:93234800-93250400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr11:93235200-93250200	Weak transcription	Aorta	Aorta
14	chr11:93235400-93257800	Weak transcription	Gastric	stomach
15	chr11:93235600-93258800	Weak transcription	Small Intestine	intestine
16	chr11:93235800-93252600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr11:93237000-93248800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr11:93238400-93248400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr11:93238400-93259000	Weak transcription	Fetal Lung	lung
20	chr11:93238600-93248800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr11:93239600-93255600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr11:93241000-93252400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr11:93241000-93254200	Weak transcription	HepG2	liver
24	chr11:93241800-93257400	Weak transcription	Fetal Intestine Large	intestine
25	chr11:93242200-93247600	Weak transcription	Fetal Stomach	stomach
26	chr11:93243200-93252200	Weak transcription	Dnd41	blood
27	chr11:93243400-93248800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:93243400-93250000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr11:93243800-93248600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr11:93243800-93255600	Weak transcription	Fetal Intestine Small	intestine
31	chr11:93244000-93248800	Weak transcription	Right Ventricle	heart
32	chr11:93244000-93254400	Weak transcription	Pancreas	Pancrea
33	chr11:93244200-93253800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr11:93244600-93246800	Flanking Active TSS	GM12878-XiMat	blood
35	chr11:93244600-93248800	Weak transcription	Fetal Thymus	thymus
36	chr11:93244600-93248800	Weak transcription	Left Ventricle	heart
37	chr11:93244600-93248800	Weak transcription	Lung	lung
38	chr11:93244800-93248400	Weak transcription	Liver	Liver
39	chr11:93244800-93254000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr11:93245800-93246800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr11:93245800-93247000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr11:93246000-93246200	Enhancers	Spleen	Spleen
43	chr11:93246000-93246400	Enhancers	Primary B cells from peripheral blood	blood

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