Variant report

Variant	rs708200
Chromosome Location	chr12:31539303-31539304
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:31538969..31541517-chr12:31543740..31545415,2	K562	blood:
2	chr12:31538215..31540416-chr12:31540541..31543060,2	K562	blood:
3	chr12:31476167..31479158-chr12:31538248..31540610,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177340	Chromatin interaction
ENSG00000139146	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1012154	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs10771828	0.81[AMR][1000 genomes]
rs10771832	0.81[CEU][hapmap]
rs10843942	0.81[AMR][1000 genomes]
rs11051418	0.81[AMR][1000 genomes]
rs1150942	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1150953	0.86[CHB][hapmap]
rs1150954	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1150955	0.89[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11615961	0.81[AMR][1000 genomes]
rs1259235	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1259356	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1259386	0.83[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs1259409	0.92[CHB][hapmap]
rs1259428	0.89[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[YRI][hapmap]
rs1259437	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1272773	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs12814351	0.80[AMR][1000 genomes]
rs1469673	0.81[AMR][1000 genomes]
rs1677189	0.82[JPT][hapmap]
rs1716216	0.89[ASW][hapmap];0.86[CHB][hapmap]
rs2116704	0.81[AMR][1000 genomes]
rs2374190	1.00[CHB][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs2568884	0.89[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2568887	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2568902	0.89[ASN][1000 genomes]
rs2604052	0.83[EUR][1000 genomes]
rs2617190	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2617191	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2617200	0.86[CHB][hapmap]
rs2682674	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2682680	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2682695	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2682697	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2682700	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2888762	0.80[AMR][1000 genomes]
rs35906870	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4931488	0.81[AMR][1000 genomes]
rs6416254	0.81[AMR][1000 genomes]
rs6487989	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs66521153	0.81[AMR][1000 genomes]
rs708209	0.89[ASW][hapmap];0.82[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs708212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs708214	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs708215	0.98[ASN][1000 genomes]
rs708217	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs708219	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7134365	0.81[AMR][1000 genomes]
rs7136476	0.84[CEU][hapmap]
rs71440988	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7294574	0.81[AMR][1000 genomes]
rs7302698	0.81[AMR][1000 genomes]
rs7303447	0.81[AMR][1000 genomes]
rs7303848	0.80[AMR][1000 genomes]
rs7313158	0.80[EUR][1000 genomes]
rs7313689	0.80[AMR][1000 genomes]
rs792871	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs792875	0.95[ASN][1000 genomes]
rs793146	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs793148	0.89[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs793150	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs793154	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs793157	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs793158	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs793161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs793174	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs793176	0.85[CHB][hapmap]
rs793177	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs793180	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs793184	0.92[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs793186	0.89[ASW][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs793191	0.92[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs7959877	0.81[AMR][1000 genomes]
rs7962896	0.81[AMR][1000 genomes]
rs7968291	0.81[AMR][1000 genomes]
rs7975761	0.81[AMR][1000 genomes]
rs809407	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs899159	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv2751046	chr12:31174233-31684733	Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv832364	chr12:31467990-31648144	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	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
rs708200	DENND5B	cis	cerebellum	SCAN
rs708200	DENND5B	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31524400-31540200	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:31530800-31541400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr12:31531800-31539600	Weak transcription	HSMM	muscle
4	chr12:31534400-31540400	Weak transcription	Psoas Muscle	Psoas
5	chr12:31534800-31541800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:31535400-31541800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:31535600-31560600	Weak transcription	Osteobl	bone
8	chr12:31535800-31539400	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:31535800-31544000	Weak transcription	Fetal Lung	lung
10	chr12:31536000-31540400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:31536000-31550600	Weak transcription	Right Ventricle	heart
12	chr12:31536400-31539800	Weak transcription	Hela-S3	cervix
13	chr12:31536400-31624600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:31536600-31547000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:31536600-31577400	Weak transcription	Small Intestine	intestine
16	chr12:31536800-31539400	Weak transcription	GM12878-XiMat	blood
17	chr12:31536800-31540400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr12:31537000-31539400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:31537000-31540200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:31537200-31540400	Weak transcription	Fetal Stomach	stomach
21	chr12:31537200-31546400	Strong transcription	Fetal Intestine Large	intestine
22	chr12:31537200-31555600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:31537400-31541200	Weak transcription	Colon Smooth Muscle	Colon
24	chr12:31537400-31545800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:31537400-31604800	Weak transcription	Spleen	Spleen
26	chr12:31537600-31541800	Weak transcription	Fetal Brain Male	brain
27	chr12:31537600-31544800	Strong transcription	Fetal Brain Female	brain
28	chr12:31537600-31580800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:31537800-31540200	Weak transcription	HepG2	liver
30	chr12:31537800-31572400	Weak transcription	Stomach Mucosa	stomach
31	chr12:31538000-31540800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr12:31538000-31540800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr12:31538000-31541800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:31538000-31544400	Strong transcription	Duodenum Mucosa	Duodenum
35	chr12:31538000-31549800	Strong transcription	A549	lung
36	chr12:31538000-31555600	Strong transcription	Liver	Liver
37	chr12:31538200-31539400	Active TSS	H9 Cell Line	embryonic stem cell
38	chr12:31538200-31540000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr12:31538200-31540400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr12:31538200-31540400	Weak transcription	Fetal Kidney	kidney
41	chr12:31538200-31540800	Strong transcription	Aorta	Aorta
42	chr12:31538200-31541000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:31538200-31542600	Strong transcription	Left Ventricle	heart
44	chr12:31538200-31544600	Strong transcription	Adipose Nuclei	Adipose
45	chr12:31538200-31545400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:31538200-31548600	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr12:31538400-31539400	Strong transcription	Ovary	ovary
48	chr12:31538400-31540000	Strong transcription	Brain Angular Gyrus	brain
49	chr12:31538400-31540400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr12:31538400-31542200	Strong transcription	Stomach Smooth Muscle	stomach

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