Variant report

Variant	rs3905238
Chromosome Location	chr4:3078937-3078938
allele	C/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	WRNIP1	chr4:3078383-3078945	GM12878	blood:	n/a	n/a
2	SPI1	chr4:3078879-3079107	GM12878	blood:	n/a	chr4:3079058-3079067 chr4:3079054-3079063
3	POLR2A	chr4:3078254-3079310	GM12878	blood:	n/a	n/a
4	POLR2A	chr4:3075327-3080089	GM18505	blood:	n/a	n/a
5	POLR2A	chr4:3076054-3080438	GM12891	blood:	n/a	n/a
6	NFIC	chr4:3078814-3080343	GM12878	blood:	n/a	n/a
7	SPI1	chr4:3078937-3079119	GM12891	blood:	n/a	chr4:3079058-3079067 chr4:3079054-3079063
8	CHD1	chr4:3078922-3079069	GM12878	blood:	n/a	n/a
9	MTA3	chr4:3076693-3080356	GM12878	blood:	n/a	n/a
10	POLR2A	chr4:3076052-3080484	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:3076735..3079040-chr4:3100560..3102807,2	K562	blood:
2	chr4:3076522..3079094-chr4:3136211..3138250,2	MCF-7	breast:
3	chr4:3076560..3079556-chr4:3107118..3109310,3	MCF-7	breast:

Variant related genes	Relation type
HTT-AS	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17780797	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2024115	0.80[EUR][1000 genomes]
rs2071655	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2285086	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28403215	0.83[EUR][1000 genomes]
rs2857935	0.90[ASN][1000 genomes]
rs28867436	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs363063	0.82[EUR][1000 genomes]
rs3856973	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4498089	0.85[ASN][1000 genomes]
rs4690011	0.82[EUR][1000 genomes]
rs4690072	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4690073	0.82[EUR][1000 genomes]
rs6446722	0.81[AMR][1000 genomes]
rs6446723	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7691627	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3075400-3079800	Active TSS	GM12878-XiMat	blood
2	chr4:3077200-3081000	Weak transcription	Spleen	Spleen
3	chr4:3077400-3079600	Weak transcription	Gastric	stomach
4	chr4:3077400-3093800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:3077600-3080000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:3077600-3081400	Weak transcription	Ovary	ovary
7	chr4:3077800-3082400	Enhancers	Primary B cells from peripheral blood	blood
8	chr4:3077800-3084400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:3077800-3089000	Weak transcription	Aorta	Aorta
10	chr4:3077800-3096400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr4:3078000-3079000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr4:3078000-3079000	Enhancers	Liver	Liver
13	chr4:3078000-3079000	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr4:3078000-3079200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:3078000-3079200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:3078000-3079600	Weak transcription	Left Ventricle	heart
17	chr4:3078000-3081000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr4:3078000-3081000	Weak transcription	Right Atrium	heart
19	chr4:3078000-3081400	Weak transcription	Right Ventricle	heart
20	chr4:3078000-3082200	Enhancers	Primary B cells from cord blood	blood
21	chr4:3078000-3083400	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr4:3078000-3084200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr4:3078000-3086200	Weak transcription	Placenta	Placenta
24	chr4:3078000-3086800	Weak transcription	Pancreas	Pancrea
25	chr4:3078000-3088000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr4:3078000-3088400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:3078000-3088600	Weak transcription	Lung	lung
28	chr4:3078000-3088800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr4:3078000-3088800	Weak transcription	Thymus	Thymus
30	chr4:3078000-3094600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:3078000-3094600	Weak transcription	Esophagus	oesophagus
32	chr4:3078000-3097400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr4:3078000-3097600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr4:3078000-3101000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr4:3078000-3103000	Weak transcription	Colonic Mucosa	Colon
36	chr4:3078200-3079000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr4:3078200-3079600	Weak transcription	Brain Angular Gyrus	brain
38	chr4:3078200-3079600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr4:3078200-3079800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr4:3078200-3079800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:3078200-3089000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:3078200-3089000	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:3078200-3094600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:3078200-3101000	Weak transcription	Brain Substantia Nigra	brain
45	chr4:3078200-3109800	Weak transcription	Stomach Mucosa	stomach
46	chr4:3078400-3079000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:3078400-3079000	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr4:3078400-3079000	Enhancers	Dnd41	blood
49	chr4:3078400-3079600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr4:3078400-3081000	Weak transcription	Monocytes-CD14+_RO01746	blood

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