Variant report

Variant	rs13129052
Chromosome Location	chr4:3300783-3300784
allele	A/G
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	chr4:3299099..3300843-chr4:3320328..3323004,2	MCF-7	breast:
3	chr4:3297687..3301019-chr4:3306995..3308843,3	K562	blood:
4	chr4:3299967..3302345-chr4:3306185..3308779,2	MCF-7	breast:
5	chr4:3299302..3301321-chr4:3301598..3303131,2	MCF-7	breast:
6	chr4:3299078..3301560-chr4:3303600..3305932,2	MCF-7	breast:
7	chr4:3294728..3297667-chr4:3300609..3302495,3	K562	blood:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1120898	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13110866	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13120043	0.82[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13126960	0.82[ASN][1000 genomes]
rs13130998	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13133859	0.82[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13150521	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844124	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844147	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844152	0.82[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16844209	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs34004517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34052318	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34067673	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34628563	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34780636	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34849917	0.82[ASN][1000 genomes]
rs35150150	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35450001	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35720136	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35825779	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57904538	0.91[ASN][1000 genomes]
rs61211078	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61748736	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71608266	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71608267	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608268	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71608278	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs878004	0.82[ASN][1000 genomes]
rs994425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs994426	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

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:61 , 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	chr4:3296000-3300800	Weak transcription	Right Atrium	heart
3	chr4:3296000-3301000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:3296000-3301000	Weak transcription	Psoas Muscle	Psoas
5	chr4:3296000-3306000	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:3296200-3300800	Weak transcription	HSMMtube	muscle
7	chr4:3296200-3301200	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr4:3296200-3301200	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:3296400-3300800	Weak transcription	Primary T cells from cord blood	blood
10	chr4:3296400-3301800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:3296600-3300800	Weak transcription	Ovary	ovary
12	chr4:3296600-3300800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr4:3296600-3301200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr4:3296800-3300800	Weak transcription	Left Ventricle	heart
16	chr4:3296800-3300800	Weak transcription	Lung	lung
17	chr4:3296800-3300800	Weak transcription	Right Ventricle	heart
18	chr4:3296800-3301400	Weak transcription	Fetal Brain Male	brain
19	chr4:3296800-3301600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:3296800-3301800	Weak transcription	Gastric	stomach
21	chr4:3296800-3306800	Weak transcription	Pancreas	Pancrea
22	chr4:3297000-3301000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:3297000-3301000	Weak transcription	Fetal Muscle Leg	muscle
24	chr4:3297000-3301200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:3297000-3301600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:3297000-3301600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr4:3298800-3300800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:3298800-3306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:3299200-3301000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:3299200-3310000	Enhancers	HUVEC	blood vessel
31	chr4:3299400-3300800	Weak transcription	Fetal Lung	lung
32	chr4:3299400-3301000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:3299400-3301000	Weak transcription	Spleen	Spleen
34	chr4:3299600-3300800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:3299600-3300800	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr4:3299600-3301000	Weak transcription	Adipose Nuclei	Adipose
37	chr4:3299600-3301000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr4:3299600-3301000	Weak transcription	Fetal Stomach	stomach
39	chr4:3299600-3301600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr4:3299600-3301800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:3299600-3302000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:3299600-3303200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:3299600-3304200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr4:3299600-3306200	Weak transcription	Fetal Intestine Small	intestine
45	chr4:3299600-3306200	Weak transcription	NHLF	lung
46	chr4:3299600-3306600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr4:3299600-3318600	Weak transcription	Aorta	Aorta
48	chr4:3299800-3302400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr4:3300000-3301000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:3300000-3301000	Weak transcription	Fetal Brain Female	brain

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