Variant report

Variant	rs644582
Chromosome Location	chr13:110840028-110840029
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2172725	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2241967	0.82[CHD][hapmap]
rs2278673	0.81[CHD][hapmap];0.86[JPT][hapmap]
rs2391816	0.86[JPT][hapmap]
rs3783106	0.81[JPT][hapmap]
rs3783107	0.81[JPT][hapmap]
rs565470	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7326444	0.86[JPT][hapmap]
rs9521638	0.83[CHD][hapmap];0.86[JPT][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs644582	C13orf29	cis	parietal	SCAN
rs644582	POU5F1P4	trans	cerebellum	SCAN
rs644582	TMEM208	trans	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	chr13:110806600-110860400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr13:110810200-110866400	Strong transcription	Stomach Smooth Muscle	stomach
8	chr13:110811000-110840200	Strong transcription	HUVEC	blood vessel
9	chr13:110816200-110840400	Strong transcription	Adipose Nuclei	Adipose
10	chr13:110822200-110840200	Strong transcription	Colon Smooth Muscle	Colon
11	chr13:110826400-110868200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr13:110826600-110858600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr13:110826600-110866200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:110826800-110847200	Strong transcription	Aorta	Aorta
15	chr13:110826800-110868000	Weak transcription	Brain Anterior Caudate	brain
16	chr13:110827000-110849200	Strong transcription	Fetal Stomach	stomach
17	chr13:110827600-110844200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr13:110827600-110869000	Weak transcription	Brain Hippocampus Middle	brain
19	chr13:110829000-110865000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr13:110829600-110874400	Weak transcription	A549	lung
21	chr13:110829800-110869600	Weak transcription	Small Intestine	intestine
22	chr13:110830000-110840400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:110830000-110870800	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr13:110830200-110869600	Weak transcription	Fetal Brain Male	brain
25	chr13:110831000-110866000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr13:110831600-110842200	Weak transcription	Liver	Liver
27	chr13:110832800-110840400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr13:110833000-110849000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:110834600-110842800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:110834600-110858400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr13:110835200-110846400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:110835200-110858600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr13:110835400-110866800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:110835600-110842000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr13:110835600-110854600	Weak transcription	Fetal Brain Female	brain
36	chr13:110835600-110858400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr13:110835800-110846000	Weak transcription	Colonic Mucosa	Colon
38	chr13:110836200-110842600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr13:110836400-110874200	Weak transcription	Esophagus	oesophagus
40	chr13:110836600-110845000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr13:110836600-110851600	Weak transcription	Brain Germinal Matrix	brain
42	chr13:110837200-110840200	Weak transcription	Stomach Mucosa	stomach
43	chr13:110837800-110840600	Genic enhancers	Fetal Intestine Small	intestine
44	chr13:110837800-110841000	Enhancers	Fetal Intestine Large	intestine
45	chr13:110837800-110841200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr13:110837800-110841200	Genic enhancers	NH-A	brain
47	chr13:110837800-110847000	Strong transcription	Lung	lung
48	chr13:110838000-110840200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr13:110838000-110840200	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr13:110838000-110841800	Genic enhancers	Fetal Muscle Trunk	muscle

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