Variant report

Variant	rs3129310
Chromosome Location	chr4:3301388-3301389
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3220220..3221940-chr4:3299861..3302041,2	MCF-7	breast:
2	chr4:3301249..3303803-chr4:3305446..3308056,2	MCF-7	breast:
3	chr4:3299967..3302345-chr4:3306185..3308779,2	MCF-7	breast:
4	chr4:3299078..3301560-chr4:3303600..3305932,2	MCF-7	breast:
5	chr4:3294728..3297667-chr4:3300609..3302495,3	K562	blood:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10155132	0.96[CEU][hapmap];0.90[JPT][hapmap]
rs10937924	0.85[EUR][1000 genomes]
rs13104157	0.85[EUR][1000 genomes]
rs2051558	0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2071666	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2157090	0.86[CHB][hapmap]
rs2236052	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2239725	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2530601	0.86[CHB][hapmap]
rs2748447	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2749780	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2749781	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs2749782	1.00[CEU][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2749783	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2749785	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs2798221	0.80[CHB][hapmap]
rs2857861	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs3095077	0.81[CHB][hapmap]
rs3129308	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3129314	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3129316	0.96[ASN][1000 genomes]
rs3129327	1.00[CEU][hapmap]
rs3129328	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3129334	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs3135064	0.82[ASN][1000 genomes]
rs3135145	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3135146	1.00[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60208975	0.85[EUR][1000 genomes]
rs6446727	0.86[CHB][hapmap]
rs6446731	0.90[CHB][hapmap]
rs6819202	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7435601	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs7661630	0.86[CHB][hapmap]
rs881816	1.00[CEU][hapmap]
rs881817	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs910568	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9996868	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3294600-3308800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:3296000-3306000	Weak transcription	Colon Smooth Muscle	Colon
3	chr4:3296400-3301800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:3296800-3301400	Weak transcription	Fetal Brain Male	brain
6	chr4:3296800-3301600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:3296800-3301800	Weak transcription	Gastric	stomach
8	chr4:3296800-3306800	Weak transcription	Pancreas	Pancrea
9	chr4:3297000-3301600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:3297000-3301600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr4:3298800-3306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:3299200-3310000	Enhancers	HUVEC	blood vessel
13	chr4:3299600-3301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:3299600-3301800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:3299600-3302000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr4:3299600-3303200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr4:3299600-3304200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:3299600-3306200	Weak transcription	Fetal Intestine Small	intestine
19	chr4:3299600-3306200	Weak transcription	NHLF	lung
20	chr4:3299600-3306600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:3299600-3318600	Weak transcription	Aorta	Aorta
22	chr4:3299800-3302400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:3300000-3303000	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr4:3300200-3302200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:3300200-3302600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:3300400-3301600	Enhancers	Fetal Kidney	kidney
27	chr4:3300600-3301800	Enhancers	HepG2	liver
28	chr4:3300600-3302200	Enhancers	Fetal Heart	heart
29	chr4:3300600-3302400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr4:3300600-3302600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr4:3300600-3303400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr4:3300600-3304400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:3300600-3306200	Enhancers	Brain Germinal Matrix	brain
34	chr4:3300800-3301400	Enhancers	Ovary	ovary
35	chr4:3300800-3301800	Enhancers	Primary hematopoietic stem cells	blood
36	chr4:3300800-3301800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr4:3300800-3301800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr4:3300800-3301800	Enhancers	Right Atrium	heart
39	chr4:3300800-3301800	Enhancers	HSMMtube	muscle
40	chr4:3300800-3302000	Enhancers	Left Ventricle	heart
41	chr4:3300800-3302600	Enhancers	Fetal Lung	lung
42	chr4:3300800-3302800	Enhancers	Right Ventricle	heart
43	chr4:3300800-3303200	Bivalent Enhancer	Fetal Thymus	thymus
44	chr4:3300800-3303800	Enhancers	Primary T cells from cord blood	blood
45	chr4:3300800-3303800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:3300800-3304000	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr4:3300800-3304600	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr4:3300800-3305400	Enhancers	Lung	lung
49	chr4:3300800-3309000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr4:3301000-3301400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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