Variant report

Variant	rs3850971
Chromosome Location	chr12:31782851-31782852
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	chr12:31776560..31779005-chr12:31780696..31784088,3	K562	blood:
2	chr12:31477438..31479159-chr12:31779343..31782901,3	K562	blood:

Variant related genes	Relation type
ENSG00000139146	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10771860	0.87[ASN][1000 genomes]
rs10843975	0.81[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10843976	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843977	0.85[ASN][1000 genomes]
rs10843980	0.88[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs10843981	0.84[ASN][1000 genomes]
rs10843982	0.81[ASN][1000 genomes]
rs10843983	0.81[ASN][1000 genomes]
rs10843984	0.84[ASN][1000 genomes]
rs10843985	0.81[ASN][1000 genomes]
rs11051491	0.85[ASN][1000 genomes]
rs11051496	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11051505	0.94[CHB][hapmap]
rs11051507	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs11051508	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs12366487	0.86[ASN][1000 genomes]
rs12368226	0.87[ASN][1000 genomes]
rs12370374	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12813290	0.94[CHB][hapmap]
rs2374165	0.94[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2374167	0.83[ASN][1000 genomes]
rs2374168	0.87[ASN][1000 genomes]
rs2374170	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2888753	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2888754	0.87[ASN][1000 genomes]
rs34312039	0.86[ASN][1000 genomes]
rs3850970	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3908176	0.88[ASN][1000 genomes]
rs3908177	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4600301	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4931531	0.83[ASN][1000 genomes]
rs4931533	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4999141	0.85[ASN][1000 genomes]
rs56320129	0.81[ASN][1000 genomes]
rs57741885	0.87[ASN][1000 genomes]
rs61930405	0.81[ASN][1000 genomes]
rs6487998	0.94[CHB][hapmap];0.88[CHD][hapmap]
rs7959945	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7962168	0.94[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs7967222	0.84[ASN][1000 genomes]
rs7974004	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7974863	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[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	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3850971	DENND5B	cis	parietal	SCAN
rs3850971	FAM71D	trans	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31781400-31783000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr12:31782200-31783000	Enhancers	Fetal Kidney	kidney
3	chr12:31782200-31783400	Enhancers	Fetal Intestine Small	intestine
4	chr12:31782200-31783400	Enhancers	Fetal Lung	lung
5	chr12:31782200-31783400	Enhancers	HepG2	liver
6	chr12:31782200-31783600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:31782200-31784600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:31782400-31783000	Enhancers	HSMMtube	muscle
9	chr12:31782400-31783000	Enhancers	NHDF-Ad	bronchial
10	chr12:31782400-31783200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr12:31782400-31783200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr12:31782400-31783200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr12:31782400-31783400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr12:31782400-31783400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:31782400-31783400	Enhancers	Psoas Muscle	Psoas
16	chr12:31782400-31783600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:31782400-31783600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:31782400-31783600	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr12:31782400-31783600	Enhancers	Pancreas	Pancrea
20	chr12:31782400-31783600	Enhancers	Right Ventricle	heart
21	chr12:31782400-31783800	Enhancers	Adipose Nuclei	Adipose
22	chr12:31782400-31783800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr12:31782400-31784000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr12:31782400-31784000	Enhancers	Fetal Stomach	stomach
25	chr12:31782400-31784000	Enhancers	Left Ventricle	heart
26	chr12:31782400-31784000	Enhancers	HSMM	muscle
27	chr12:31782400-31784600	Enhancers	Fetal Muscle Leg	muscle
28	chr12:31782600-31783000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:31782600-31783000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:31782600-31783000	Enhancers	A549	lung
31	chr12:31782600-31783000	Enhancers	NH-A	brain
32	chr12:31782600-31783000	Enhancers	Osteobl	bone
33	chr12:31782600-31783200	Enhancers	Right Atrium	heart
34	chr12:31782600-31783400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:31782600-31783400	Flanking Active TSS	Fetal Heart	heart
36	chr12:31782600-31783400	Enhancers	Placenta	Placenta
37	chr12:31782600-31783600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:31782600-31783600	Enhancers	HUVEC	blood vessel
39	chr12:31782800-31783000	Flanking Active TSS	Ovary	ovary
40	chr12:31782800-31783000	Flanking Active TSS	Rectal Smooth Muscle	rectum
41	chr12:31782800-31783000	Flanking Active TSS	K562	blood
42	chr12:31782800-31783200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr12:31782800-31783200	Flanking Active TSS	Colon Smooth Muscle	Colon
44	chr12:31782800-31783400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:31782800-31783600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr12:31782800-31783600	Flanking Active TSS	Stomach Smooth Muscle	stomach

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