Variant report

Variant	rs9521638
Chromosome Location	chr13:110839428-110839429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1000989	0.95[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1000990	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1562173	0.96[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1562174	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16975472	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16975491	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16975492	0.96[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1891964	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1975514	0.96[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1977892	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1977893	0.83[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2005447	0.96[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2131937	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2131938	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172725	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2278673	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289799	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2289800	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2305080	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391815	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2391816	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2391817	0.80[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3783105	0.90[CEU][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783106	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783107	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783111	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3783113	1.00[CEU][hapmap];0.86[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs503053	0.92[CEU][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs644582	0.83[CHD][hapmap];0.86[JPT][hapmap]
rs7325512	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7329411	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs874203	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs874204	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9515160	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9515161	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9521632	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9521633	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9521634	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9521635	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9521636	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9521637	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9588108	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	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
3	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
4	nsv1182	chr13:110829691-110875029	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9521638	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	chr13:110802400-110842800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:110803000-110840400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr13:110803200-110839800	Weak transcription	NHDF-Ad	bronchial
7	chr13:110803200-110839800	Strong transcription	Osteobl	bone
8	chr13:110803600-110840000	Strong transcription	Muscle Satellite Cultured Cells	--
9	chr13:110806600-110860400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr13:110809200-110840000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:110810200-110866400	Strong transcription	Stomach Smooth Muscle	stomach
12	chr13:110811000-110840200	Strong transcription	HUVEC	blood vessel
13	chr13:110816200-110840400	Strong transcription	Adipose Nuclei	Adipose
14	chr13:110822000-110839800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:110822200-110840000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:110822200-110840200	Strong transcription	Colon Smooth Muscle	Colon
17	chr13:110823000-110840000	Strong transcription	Fetal Lung	lung
18	chr13:110826400-110839600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:110826400-110868200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr13:110826600-110858600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr13:110826600-110866200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr13:110826800-110847200	Strong transcription	Aorta	Aorta
23	chr13:110826800-110868000	Weak transcription	Brain Anterior Caudate	brain
24	chr13:110827000-110839600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:110827000-110849200	Strong transcription	Fetal Stomach	stomach
26	chr13:110827600-110844200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr13:110827600-110869000	Weak transcription	Brain Hippocampus Middle	brain
28	chr13:110829000-110865000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:110829600-110874400	Weak transcription	A549	lung
30	chr13:110829800-110869600	Weak transcription	Small Intestine	intestine
31	chr13:110830000-110840400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:110830000-110870800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr13:110830200-110869600	Weak transcription	Fetal Brain Male	brain
34	chr13:110831000-110866000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr13:110831600-110842200	Weak transcription	Liver	Liver
36	chr13:110832200-110839600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr13:110832800-110840400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr13:110833000-110849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:110834600-110842800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:110834600-110858400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr13:110835200-110846400	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr13:110835200-110858600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr13:110835400-110866800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr13:110835600-110842000	Genic enhancers	Fetal Muscle Leg	muscle
45	chr13:110835600-110854600	Weak transcription	Fetal Brain Female	brain
46	chr13:110835600-110858400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr13:110835800-110846000	Weak transcription	Colonic Mucosa	Colon
48	chr13:110836200-110842600	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr13:110836400-110874200	Weak transcription	Esophagus	oesophagus
50	chr13:110836600-110845000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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