Variant report

Variant	rs3135145
Chromosome Location	chr4:3299504-3299505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3293263..3296251-chr4:3298199..3300477,2	K562	blood:
2	chr4:3299099..3300843-chr4:3320328..3323004,2	MCF-7	breast:
3	chr4:3298898..3300688-chr4:3301683..3304655,2	K562	blood:
4	chr4:3297687..3301019-chr4:3306995..3308843,3	K562	blood:
5	chr4:3297413..3300399-chr4:3305342..3309576,4	MCF-7	breast:
6	chr4:3299302..3301321-chr4:3301598..3303131,2	MCF-7	breast:
7	chr4:3299078..3301560-chr4:3303600..3305932,2	MCF-7	breast:
8	chr4:3297878..3299647-chr4:3439847..3442316,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10155132	0.92[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap]
rs10937924	0.85[EUR][1000 genomes]
rs13104157	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13150241	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2051558	0.83[JPT][hapmap]
rs2071666	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2071671	0.83[CHB][hapmap]
rs2157090	0.80[CHB][hapmap]
rs2236052	0.96[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2239725	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2530601	0.80[CHB][hapmap]
rs2748447	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2749778	0.83[ASN][1000 genomes]
rs2749780	0.85[EUR][1000 genomes]
rs2749781	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2749782	0.96[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2749783	0.95[CEU][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2749785	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2798221	0.84[CHB][hapmap]
rs2857982	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3095077	0.84[CHB][hapmap]
rs3129308	0.96[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129310	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]
rs3129314	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3129316	0.88[ASN][1000 genomes]
rs3129327	0.96[CEU][hapmap];0.89[CHB][hapmap]
rs3129328	0.96[CEU][hapmap];0.81[CHB][hapmap]
rs3129334	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs3135146	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60181496	0.82[EUR][1000 genomes]
rs60208975	0.86[EUR][1000 genomes]
rs6446727	0.80[CHB][hapmap]
rs6819202	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7435601	0.96[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7661630	0.80[CHB][hapmap]
rs881816	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[EUR][1000 genomes]
rs881817	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs910568	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[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:60 , 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	chr4:3295600-3300600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:3296000-3300800	Weak transcription	Right Atrium	heart
4	chr4:3296000-3301000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:3296000-3301000	Weak transcription	Psoas Muscle	Psoas
6	chr4:3296000-3306000	Weak transcription	Colon Smooth Muscle	Colon
7	chr4:3296200-3300800	Weak transcription	HSMMtube	muscle
8	chr4:3296200-3301200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:3296200-3301200	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:3296400-3299600	ZNF genes & repeats	Fetal Stomach	stomach
11	chr4:3296400-3300800	Weak transcription	Primary T cells from cord blood	blood
12	chr4:3296400-3301800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr4:3296600-3300600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr4:3296600-3300800	Weak transcription	Ovary	ovary
15	chr4:3296600-3300800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:3296600-3301200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr4:3296600-3318600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:3296800-3300600	Weak transcription	Fetal Heart	heart
19	chr4:3296800-3300800	Weak transcription	Left Ventricle	heart
20	chr4:3296800-3300800	Weak transcription	Lung	lung
21	chr4:3296800-3300800	Weak transcription	Right Ventricle	heart
22	chr4:3296800-3301400	Weak transcription	Fetal Brain Male	brain
23	chr4:3296800-3301600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr4:3296800-3301800	Weak transcription	Gastric	stomach
25	chr4:3296800-3306800	Weak transcription	Pancreas	Pancrea
26	chr4:3297000-3300400	Weak transcription	Fetal Kidney	kidney
27	chr4:3297000-3300600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr4:3297000-3301000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr4:3297000-3301000	Weak transcription	Fetal Muscle Leg	muscle
30	chr4:3297000-3301200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr4:3297000-3301600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:3297000-3301600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr4:3297600-3299600	ZNF genes & repeats	Brain Germinal Matrix	brain
34	chr4:3297600-3299600	Strong transcription	Fetal Intestine Small	intestine
35	chr4:3298200-3299600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:3298200-3299600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:3298200-3299600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:3298200-3299800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:3298200-3300000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr4:3298200-3300000	ZNF genes & repeats	Fetal Brain Female	brain
41	chr4:3298400-3299600	ZNF genes & repeats	Aorta	Aorta
42	chr4:3298800-3299600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr4:3298800-3300600	Weak transcription	HepG2	liver
44	chr4:3298800-3300800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr4:3298800-3306400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:3299000-3299600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr4:3299200-3299600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr4:3299200-3299600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:3299200-3299600	Enhancers	Adipose Nuclei	Adipose
50	chr4:3299200-3299600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain

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