Variant report

Variant	rs10845474
Chromosome Location	chr12:12238317-12238318
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	chr12:12237772..12239926-chr12:12242513..12244512,2	K562	blood:

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10845472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10845473	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10845478	0.83[MEX][hapmap]
rs11054673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054674	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11054675	0.84[ASN][1000 genomes]
rs11054676	0.84[ASN][1000 genomes]
rs11054677	0.85[ASN][1000 genomes]
rs11054678	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs11054680	0.85[ASN][1000 genomes]
rs2287155	0.85[ASN][1000 genomes]
rs73053308	0.85[ASN][1000 genomes]
rs7959836	0.96[CEU][hapmap];0.84[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs7962856	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972500	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973469	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs884139	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs885637	0.92[CHD][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv975623	chr12:12238184-12243964	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv557583	chr12:12238317-12253591	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10845474	DUSP16	cis	cerebellum	SCAN
rs10845474	CD69	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12225000-12255000	Weak transcription	Small Intestine	intestine
2	chr12:12225200-12239400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr12:12225400-12239000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:12225400-12239600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:12225400-12239600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:12225600-12239000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr12:12225800-12240200	Weak transcription	Fetal Stomach	stomach
8	chr12:12226600-12245000	Weak transcription	Fetal Brain Male	brain
9	chr12:12229600-12238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:12230000-12238600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:12231000-12239200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:12231400-12238600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr12:12231400-12239200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:12231600-12239200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:12232800-12240000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:12232800-12257000	Weak transcription	HSMMtube	muscle
17	chr12:12234800-12259600	Weak transcription	Aorta	Aorta
18	chr12:12235200-12242000	Weak transcription	NHLF	lung
19	chr12:12235400-12239400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:12235400-12239800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:12235400-12243600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr12:12235400-12244600	Weak transcription	Colonic Mucosa	Colon
23	chr12:12235400-12245000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:12235400-12245200	Weak transcription	Pancreas	Pancrea
25	chr12:12235400-12260200	Weak transcription	Gastric	stomach
26	chr12:12235400-12260800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:12235400-12278800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:12235600-12240800	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr12:12236400-12239200	Strong transcription	Fetal Intestine Small	intestine
30	chr12:12236400-12239400	Weak transcription	HepG2	liver
31	chr12:12236400-12240000	Weak transcription	Stomach Mucosa	stomach
32	chr12:12237000-12238800	Strong transcription	Fetal Intestine Large	intestine
33	chr12:12237200-12239600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr12:12237400-12259800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:12237600-12238600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:12238000-12245000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr12:12238200-12238400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr12:12238200-12240000	Genic enhancers	Rectal Mucosa Donor 31	rectum

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