Variant report

Variant	rs12368209
Chromosome Location	chr12:104180872-104180873
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	chr12:104177175..104180567-chr12:104180842..104183516,3	K562	blood:

Variant related genes	Relation type
ENSG00000111696	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10082821	1.00[ASN][1000 genomes]
rs10778288	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10778289	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];1.00[ASN][1000 genomes]
rs10861113	0.87[ASN][1000 genomes]
rs10861115	1.00[ASN][1000 genomes]
rs10861118	1.00[ASN][1000 genomes]
rs10861119	1.00[ASN][1000 genomes]
rs11111760	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs11111780	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11111790	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11111794	1.00[ASN][1000 genomes]
rs11111797	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11111803	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12369835	1.00[ASN][1000 genomes]
rs12426059	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs3087891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4964787	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]
rs7138889	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs7315948	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899480	chr12:104092996-104211440	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv899481	chr12:104092996-104213731	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv899482	chr12:104092996-104218956	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv34031	chr12:104114277-104298546	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
5	nsv899483	chr12:104117462-104218956	Weak transcription ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv899487	chr12:104118587-104218956	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv899489	chr12:104144835-104218956	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv899490	chr12:104149022-104218956	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv899492	chr12:104151560-104183658	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv560039	chr12:104177668-104455340	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12368209	SLC5A8	cis	parietal	SCAN
rs12368209	NT5DC3	cis	thalamus	BrainEAC
rs12368209	NT5DC3	cis	temporal cortex	BrainEAC
rs12368209	NT5DC3	cis	Whole Blood	GTEx
rs12368209	NT5DC3	cis	intralobular white matter	BrainEAC
rs12368209	IGF1	cis	parietal	SCAN
rs12368209	NT5DC3	cis	multi-tissue	Pritchard
rs12368209	NT5DC3	cis	hippocampus	BrainEAC
rs12368209	NT5DC3	cis	brain	BrainEAC

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104153200-104185200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:104154400-104186400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr12:104157400-104191200	Weak transcription	HUVEC	blood vessel
4	chr12:104160400-104185800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:104163600-104185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr12:104163600-104204200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr12:104165800-104193400	Weak transcription	Fetal Lung	lung
8	chr12:104166400-104188400	Weak transcription	Fetal Thymus	thymus
9	chr12:104167200-104199800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:104168000-104185200	Weak transcription	Brain Germinal Matrix	brain
11	chr12:104168000-104190800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:104169000-104197800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:104169600-104184800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr12:104171200-104193600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:104171400-104188200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:104171600-104187400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:104171600-104194000	Weak transcription	Brain Substantia Nigra	brain
18	chr12:104171800-104187600	Weak transcription	Fetal Brain Female	brain
19	chr12:104171800-104216000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:104172400-104186400	Weak transcription	Brain Hippocampus Middle	brain
21	chr12:104172400-104191400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr12:104173800-104208800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:104174000-104194200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:104174200-104185200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr12:104174200-104186200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:104175000-104187000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr12:104175200-104190000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr12:104176800-104181200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:104177000-104182800	Strong transcription	NH-A	brain
30	chr12:104177800-104207600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:104178200-104186400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:104178200-104187600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:104178400-104185400	Weak transcription	Right Ventricle	heart
34	chr12:104178400-104185600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:104178400-104188400	Weak transcription	Brain Anterior Caudate	brain
36	chr12:104178600-104193400	Weak transcription	Left Ventricle	heart
37	chr12:104178800-104185400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr12:104178800-104185400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:104178800-104186400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr12:104178800-104186600	Weak transcription	Colonic Mucosa	Colon
41	chr12:104178800-104194000	Weak transcription	Brain Angular Gyrus	brain
42	chr12:104178800-104194200	Weak transcription	Esophagus	oesophagus
43	chr12:104179000-104184800	Weak transcription	Fetal Stomach	stomach
44	chr12:104179000-104185000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:104179000-104185000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:104179000-104185000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr12:104179000-104185000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr12:104179000-104185200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr12:104179000-104185200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:104179000-104185400	Weak transcription	Ovary	ovary

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