Variant report

Variant	rs3886352
Chromosome Location	chr13:96332651-96332652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr13:96332616-96332654	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
DNAJC3-AS1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11616953	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11618323	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12428035	0.81[CHD][hapmap]
rs12430152	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12583796	0.86[LWK][hapmap];0.96[YRI][hapmap]
rs12855055	0.83[AFR][1000 genomes]
rs16951334	0.90[CHD][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.85[EUR][1000 genomes]
rs17878753	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17879875	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17885081	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3087341	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099362	0.90[CHD][hapmap];0.88[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3099363	0.88[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3101570	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35740456	0.86[AFR][1000 genomes]
rs3848077	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3901894	0.85[LWK][hapmap];0.96[YRI][hapmap]
rs4347496	0.84[EUR][1000 genomes]
rs4383020	0.91[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap]
rs4409947	1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4491364	0.87[ASN][1000 genomes]
rs4526890	0.84[EUR][1000 genomes]
rs6492821	0.86[LWK][hapmap];0.96[YRI][hapmap]
rs7316996	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7318892	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7323408	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7331211	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7331549	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7334552	0.83[LWK][hapmap];0.96[YRI][hapmap]
rs7991405	0.87[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9302084	0.96[YRI][hapmap]
rs9561931	0.93[YRI][hapmap];0.86[AFR][1000 genomes]
rs9561939	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9584324	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9590310	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9590328	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3886352	DZIP1	Cis_1M	lymphoblastoid	RTeQTL
rs3886352	DZIP1	cis	parietal	SCAN
rs3886352	UGGT2	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96330200-96333200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr13:96330200-96340800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:96330600-96336400	Weak transcription	Gastric	stomach
4	chr13:96330600-96336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr13:96330600-96340800	Weak transcription	Spleen	Spleen
6	chr13:96330800-96333600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr13:96330800-96333800	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr13:96330800-96334400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr13:96330800-96334400	Weak transcription	Fetal Brain Female	brain
10	chr13:96330800-96336000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr13:96330800-96336800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr13:96330800-96337000	Weak transcription	Lung	lung
13	chr13:96331000-96333400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr13:96331000-96336400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr13:96331000-96336400	Weak transcription	Fetal Stomach	stomach
16	chr13:96331200-96333000	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr13:96331200-96333000	Enhancers	Liver	Liver
18	chr13:96331200-96333200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr13:96331200-96335000	Weak transcription	Fetal Muscle Leg	muscle
20	chr13:96331200-96336400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr13:96331200-96336800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:96331200-96336800	Weak transcription	Fetal Intestine Small	intestine
23	chr13:96331200-96336800	Weak transcription	Placenta	Placenta
24	chr13:96331200-96337000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr13:96331200-96339400	Weak transcription	Fetal Muscle Trunk	muscle
26	chr13:96331400-96333200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:96331400-96333400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:96331400-96333600	Enhancers	Primary T cells from cord blood	blood
29	chr13:96331400-96333600	Weak transcription	Pancreas	Pancrea
30	chr13:96331400-96334000	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr13:96331400-96335000	Enhancers	HepG2	liver
32	chr13:96331400-96336400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr13:96331400-96336400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr13:96331400-96336400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr13:96331400-96336400	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr13:96331400-96336400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr13:96331400-96336800	Weak transcription	Left Ventricle	heart
38	chr13:96331400-96337000	Weak transcription	Ovary	ovary
39	chr13:96331400-96337000	Weak transcription	Right Ventricle	heart
40	chr13:96331400-96350600	Weak transcription	Aorta	Aorta
41	chr13:96331400-96362200	Weak transcription	HSMM	muscle
42	chr13:96331600-96333200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:96331600-96336200	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr13:96331600-96336800	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr13:96331800-96332800	Weak transcription	Psoas Muscle	Psoas
46	chr13:96331800-96332800	Weak transcription	Stomach Mucosa	stomach
47	chr13:96331800-96333400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr13:96331800-96334400	Weak transcription	Colon Smooth Muscle	Colon
49	chr13:96331800-96335600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr13:96331800-96336200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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