Variant report

Variant	rs3129330
Chromosome Location	chr4:3379380-3379381
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	chr4:3377820..3379828-chr4:3379979..3381603,2	MCF-7	breast:
2	chr4:3378617..3381558-chr4:3387314..3389192,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12640186	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12640526	0.86[ASN][1000 genomes]
rs12640721	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12643903	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16844197	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs16844201	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2073286	0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.86[ASN][1000 genomes]
rs2281470	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2343799	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749775	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2749776	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2749779	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2749786	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2857859	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2857860	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3129329	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129331	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129332	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3129333	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3129336	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58949283	0.89[ASN][1000 genomes]
rs62274923	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62274924	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73193371	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73193372	0.90[ASN][1000 genomes]
rs881818	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3129330	DOK7	cis	cerebellum	SCAN
rs3129330	HGFAC	cis	cerebellum	SCAN
rs3129330	RGS12	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3372200-3382000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:3372200-3386400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:3372400-3382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:3373000-3389000	Weak transcription	Psoas Muscle	Psoas
5	chr4:3373400-3380800	Weak transcription	Brain Angular Gyrus	brain
6	chr4:3373400-3382000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr4:3373400-3388400	Weak transcription	Fetal Kidney	kidney
8	chr4:3373400-3388800	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:3374400-3379800	Weak transcription	Fetal Lung	lung
10	chr4:3374400-3380800	Weak transcription	Fetal Brain Male	brain
11	chr4:3374600-3379800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr4:3374600-3380000	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr4:3374800-3379600	Strong transcription	Fetal Intestine Small	intestine
14	chr4:3375000-3389200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:3375200-3379600	Weak transcription	Colonic Mucosa	Colon
16	chr4:3375200-3379600	Strong transcription	Fetal Stomach	stomach
17	chr4:3375200-3381400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:3375200-3387000	Weak transcription	Right Atrium	heart
19	chr4:3375400-3380600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:3375400-3381200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr4:3375400-3386200	Weak transcription	Right Ventricle	heart
22	chr4:3375400-3386400	Weak transcription	Brain Substantia Nigra	brain
23	chr4:3375400-3386600	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:3375400-3389600	Weak transcription	NHLF	lung
25	chr4:3375600-3380000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:3375600-3380200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr4:3375600-3380600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:3375600-3381600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:3375600-3386200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr4:3375600-3387000	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr4:3376000-3381400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr4:3376000-3381800	Weak transcription	Esophagus	oesophagus
33	chr4:3376200-3380400	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr4:3376200-3380600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr4:3377400-3381200	Strong transcription	HepG2	liver
36	chr4:3377600-3383600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:3377800-3381800	Weak transcription	Brain Anterior Caudate	brain
38	chr4:3378000-3381200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr4:3378200-3379400	Weak transcription	HSMMtube	muscle
40	chr4:3378200-3380800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr4:3378200-3381200	Weak transcription	Fetal Intestine Large	intestine
42	chr4:3378200-3381800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr4:3378200-3388800	Weak transcription	Fetal Heart	heart
44	chr4:3378400-3379800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr4:3378400-3381800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr4:3378400-3381800	Weak transcription	Adipose Nuclei	Adipose
47	chr4:3378400-3382200	Weak transcription	Gastric	stomach
48	chr4:3378400-3386400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr4:3378400-3388800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr4:3378400-3389000	Weak transcription	Muscle Satellite Cultured Cells	--

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