Variant report

Variant	rs1562173
Chromosome Location	chr13:110828922-110828923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:110826571..110829024-chr13:110829639..110833128,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1000989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1000990	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1562174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16975491	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16975492	0.81[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1891964	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1975514	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1977892	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1977893	0.96[CEU][hapmap];0.92[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2005447	1.00[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131937	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2131938	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2172725	0.96[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2278673	0.96[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2289799	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289800	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305080	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2391815	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2391816	0.96[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2391817	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3783105	0.85[CEU][hapmap]
rs3783106	0.83[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs3783107	0.87[CEU][hapmap];0.80[AMR][1000 genomes]
rs3783111	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3783113	0.96[CEU][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs503053	0.96[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7325512	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7326444	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7329411	0.96[CEU][hapmap];0.83[GIH][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs874203	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs874204	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9515160	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9515161	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9521632	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9521633	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9521634	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9521635	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9521636	1.00[CEU][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9521637	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9521638	0.96[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9588108	0.94[AMR][1000 genomes];0.89[EUR][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	nsv1052147	chr13:110765635-110917782	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1045170	chr13:110815422-110836716	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv456116	chr13:110818598-110856153	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv563101	chr13:110818598-110856153	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1562173	COL4A1	cis	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110791400-110868400	Weak transcription	Psoas Muscle	Psoas
2	chr13:110798800-110853200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:110799600-110840200	Strong transcription	Duodenum Smooth Muscle	Duodenum
4	chr13:110800200-110837800	Strong transcription	NH-A	brain
5	chr13:110800600-110834200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr13:110802400-110842800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:110803000-110834200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:110803000-110840400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr13:110803200-110839800	Weak transcription	NHDF-Ad	bronchial
10	chr13:110803200-110839800	Strong transcription	Osteobl	bone
11	chr13:110803600-110840000	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr13:110806600-110860400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr13:110809200-110840000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:110809800-110831200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr13:110810200-110866400	Strong transcription	Stomach Smooth Muscle	stomach
16	chr13:110811000-110840200	Strong transcription	HUVEC	blood vessel
17	chr13:110811600-110830600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:110811800-110838800	Strong transcription	Right Ventricle	heart
19	chr13:110812000-110838800	Strong transcription	Left Ventricle	heart
20	chr13:110814200-110830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr13:110816200-110840400	Strong transcription	Adipose Nuclei	Adipose
22	chr13:110820600-110832200	Strong transcription	HSMMtube	muscle
23	chr13:110821000-110839400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:110821200-110831000	Strong transcription	NHLF	lung
25	chr13:110821200-110831200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:110822000-110839800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:110822200-110840000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:110822200-110840200	Strong transcription	Colon Smooth Muscle	Colon
29	chr13:110822600-110831800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:110822600-110832000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr13:110822800-110837800	Strong transcription	HSMM	muscle
32	chr13:110823000-110829200	Strong transcription	NHEK	skin
33	chr13:110823000-110831400	Strong transcription	HMEC	breast
34	chr13:110823000-110831800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr13:110823000-110837000	Strong transcription	Rectal Smooth Muscle	rectum
36	chr13:110823000-110840000	Strong transcription	Fetal Lung	lung
37	chr13:110823200-110831000	Strong transcription	Fetal Kidney	kidney
38	chr13:110823400-110831200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr13:110824000-110831000	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr13:110824000-110831000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr13:110824400-110829600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr13:110824400-110830000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr13:110824400-110830400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr13:110824400-110831600	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr13:110824600-110835800	Strong transcription	Placenta	Placenta
46	chr13:110824600-110836200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr13:110824800-110830800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr13:110825400-110830000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr13:110825600-110831400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:110825800-110830800	Strong transcription	H9 Cell Line	embryonic stem cell

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