Variant report

Variant	rs7963397
Chromosome Location	chr12:32658637-32658638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10743797	0.87[CEU][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10771962	0.81[CEU][hapmap]
rs10771963	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11052032	0.93[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs11052034	0.82[LWK][hapmap];0.82[MKK][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes]
rs12579931	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs2088809	0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4931632	0.94[AFR][1000 genomes]
rs7295095	0.83[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs7308412	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7980242	0.82[CEU][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1054191	chr12:32534619-32733066	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv541455	chr12:32534619-32733066	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	esv3342938	chr12:32551041-32716745	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv898970	chr12:32622097-32680236	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7963397	SYT10	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32594600-32659000	Weak transcription	Esophagus	oesophagus
2	chr12:32649000-32660800	Weak transcription	Thymus	Thymus
3	chr12:32650800-32659200	Weak transcription	Aorta	Aorta
4	chr12:32654400-32659400	Enhancers	HMEC	breast
5	chr12:32655000-32658800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:32655000-32658800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:32655200-32661600	Weak transcription	Spleen	Spleen
8	chr12:32655200-32686000	Weak transcription	Lung	lung
9	chr12:32655400-32661000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:32655800-32659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:32656000-32659200	Enhancers	Adipose Nuclei	Adipose
12	chr12:32656000-32661000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:32656000-32666000	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:32656000-32668000	Weak transcription	Fetal Thymus	thymus
15	chr12:32656200-32659800	Enhancers	H1 Cell Line	embryonic stem cell
16	chr12:32656200-32662600	Weak transcription	HepG2	liver
17	chr12:32656200-32668000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:32656400-32659400	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr12:32656400-32659400	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr12:32656400-32659800	Enhancers	Fetal Lung	lung
21	chr12:32656400-32660000	Enhancers	Fetal Intestine Small	intestine
22	chr12:32656400-32685800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:32656800-32659000	Enhancers	Stomach Mucosa	stomach
24	chr12:32656800-32659800	Enhancers	Fetal Intestine Large	intestine
25	chr12:32657000-32659600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr12:32657000-32659600	Enhancers	Psoas Muscle	Psoas
27	chr12:32657000-32661000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr12:32657000-32661800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr12:32657200-32658800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr12:32657200-32658800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr12:32657200-32659800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:32657200-32662200	Enhancers	Fetal Heart	heart
33	chr12:32657400-32659000	Flanking Active TSS	HUVEC	blood vessel
34	chr12:32657400-32659400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr12:32657400-32659400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:32657400-32659600	Enhancers	Liver	Liver
37	chr12:32657400-32659800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr12:32657400-32661400	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr12:32657600-32659400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:32657600-32659600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr12:32657800-32659600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:32658000-32658800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
43	chr12:32658000-32659000	Enhancers	Primary hematopoietic stem cells	blood
44	chr12:32658000-32659600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr12:32658000-32659600	Enhancers	Ovary	ovary
46	chr12:32658200-32658800	Enhancers	Primary T cells from cord blood	blood
47	chr12:32658200-32658800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:32658200-32658800	Flanking Active TSS	Fetal Stomach	stomach
49	chr12:32658200-32658800	Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr12:32658200-32659000	Weak transcription	H9 Cell Line	embryonic stem cell

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