Variant report

Variant	rs34945363
Chromosome Location	chr4:3044477-3044478
allele	G/T
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	YY1	chr4:3044351-3045372	H1-hESC	embryonic stem cell:	n/a	chr4:3045062-3045074 chr4:3044462-3044473
2	YY1	chr4:3044395-3044672	GM12891	blood:	n/a	chr4:3044462-3044473
3	YY1	chr4:3044388-3044704	H1-hESC	embryonic stem cell:	n/a	chr4:3044462-3044473
4	MAX	chr4:3044344-3044776	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr4:3041640-3044734	GM12891	blood:	n/a	n/a
6	POLR2A	chr4:3042157-3044616	GM12878	blood:	n/a	n/a
7	SP1	chr4:3044441-3044850	H1-hESC	embryonic stem cell:	n/a	chr4:3044457-3044471
8	POLR2A	chr4:3042124-3044657	GM18505	blood:	n/a	n/a
9	TEAD4	chr4:3044455-3044865	H1-hESC	embryonic stem cell:	n/a	n/a
10	YY1	chr4:3044337-3044749	GM12878	blood:	n/a	chr4:3044462-3044473
11	TCF12	chr4:3044417-3044697	H1-hESC	embryonic stem cell:	n/a	n/a
12	PML	chr4:3042040-3044617	GM12878	blood:	n/a	chr4:3043770-3043778

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3038856..3040749-chr4:3043216..3045055,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-204P	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10021325	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11929936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506200	0.87[ASN][1000 genomes]
rs13141939	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13144633	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2471342	0.98[ASN][1000 genomes]
rs34020100	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34053308	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34157939	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34342095	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35342954	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35875899	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61114397	0.84[ASN][1000 genomes]
rs61407336	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7694687	0.93[ASN][1000 genomes]
rs7696040	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3042400-3044600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:3042400-3044600	Flanking Active TSS	GM12878-XiMat	blood
3	chr4:3042600-3044600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:3042600-3044600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr4:3042800-3044600	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr4:3042800-3044600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr4:3042800-3044600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
8	chr4:3043000-3044600	Flanking Active TSS	HSMMtube	muscle
9	chr4:3043200-3045000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:3043200-3046000	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr4:3043600-3045600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:3043600-3047400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:3043800-3044600	Enhancers	H1 Cell Line	embryonic stem cell
14	chr4:3043800-3044600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr4:3043800-3044600	Enhancers	HMEC	breast
16	chr4:3043800-3044600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr4:3044000-3044600	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr4:3044000-3044600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr4:3044000-3044600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr4:3044000-3044600	Enhancers	Gastric	stomach
21	chr4:3044000-3044600	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr4:3044000-3044600	Enhancers	Spleen	Spleen
23	chr4:3044000-3044800	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr4:3044000-3044800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:3044000-3044800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr4:3044000-3044800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr4:3044000-3044800	Enhancers	Right Ventricle	heart
28	chr4:3044000-3045600	Enhancers	Fetal Heart	heart
29	chr4:3044000-3046800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr4:3044000-3048600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr4:3044000-3049400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:3044200-3044600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
33	chr4:3044200-3044600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr4:3044200-3044600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr4:3044200-3044600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:3044200-3044600	Enhancers	Brain Substantia Nigra	brain
37	chr4:3044200-3044600	Bivalent Enhancer	Colonic Mucosa	Colon
38	chr4:3044200-3044600	Flanking Active TSS	Colon Smooth Muscle	Colon
39	chr4:3044200-3044600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr4:3044200-3044600	Enhancers	Esophagus	oesophagus
41	chr4:3044200-3044600	Enhancers	Fetal Intestine Small	intestine
42	chr4:3044200-3044600	Bivalent Enhancer	Fetal Stomach	stomach
43	chr4:3044200-3044600	Enhancers	Lung	lung
44	chr4:3044200-3044600	Enhancers	Ovary	ovary
45	chr4:3044200-3044600	Bivalent Enhancer	HepG2	liver
46	chr4:3044200-3044800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:3044200-3044800	Enhancers	Primary monocytes fromperipheralblood	blood
48	chr4:3044200-3044800	Enhancers	Fetal Muscle Leg	muscle
49	chr4:3044200-3044800	Enhancers	Pancreas	Pancrea
50	chr4:3044200-3044800	Enhancers	Psoas Muscle	Psoas

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