Variant report

Variant	rs1371798
Chromosome Location	chr4:74976781-74976782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:74976664-74976863	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:74976407..74978358-chr4:74989024..74991226,2	K562	blood:
2	chr4:74976042..74977879-chr4:75018790..75020773,2	K562	blood:
3	chr4:74969971..74972171-chr4:74976711..74978462,2	K562	blood:
4	chr4:74905779..74908851-chr4:74974510..74977216,3	K562	blood:
5	chr4:74975738..74977942-chr4:74982143..74984309,2	K562	blood:
6	chr4:74975401..74977757-chr4:74979234..74981426,2	K562	blood:

No data

Variant related genes	Relation type
MTHFD2L	TF binding region
ENSG00000163738	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10938107	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs11725704	0.81[EUR][1000 genomes]
rs11733208	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs12642974	0.91[CEU][hapmap];0.90[EUR][1000 genomes]
rs13124617	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13128896	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1371794	0.81[EUR][1000 genomes]
rs1371799	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1837559	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1866755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4121652	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs491641	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs518867	0.81[EUR][1000 genomes]
rs546829	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs549280	0.94[EUR][1000 genomes]
rs72652928	0.80[EUR][1000 genomes]
rs72652934	0.93[EUR][1000 genomes]
rs7667376	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7684973	0.82[JPT][hapmap]
rs7686861	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs882638	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs981458	0.90[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	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active 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 lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74966800-74978000	Weak transcription	Gastric	stomach
2	chr4:74971200-74977200	Enhancers	Fetal Intestine Small	intestine
3	chr4:74971800-74977800	Weak transcription	Brain Anterior Caudate	brain
4	chr4:74972000-74982000	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:74972200-74978000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:74972800-74980200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:74973000-74978600	Enhancers	HUVEC	blood vessel
8	chr4:74973400-74980200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:74973800-74977200	Enhancers	Fetal Intestine Large	intestine
10	chr4:74974200-74981000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr4:74974400-74978000	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr4:74974600-74978000	Weak transcription	Brain Hippocampus Middle	brain
13	chr4:74974800-74977200	Enhancers	Liver	Liver
14	chr4:74975200-74977800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr4:74975400-74977600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:74975400-74977600	Weak transcription	Right Atrium	heart
17	chr4:74975400-74977800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:74975400-74978000	Weak transcription	Aorta	Aorta
19	chr4:74975600-74977400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:74975600-74977400	Weak transcription	Fetal Muscle Leg	muscle
21	chr4:74975600-74977400	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:74975600-74978000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr4:74975600-74978000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr4:74975600-74978000	Weak transcription	Pancreas	Pancrea
25	chr4:74975600-74980000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:74975600-74980800	Enhancers	NHDF-Ad	bronchial
27	chr4:74975800-74977000	Weak transcription	Stomach Mucosa	stomach
28	chr4:74975800-74977400	Weak transcription	Esophagus	oesophagus
29	chr4:74975800-74977400	Enhancers	NHEK	skin
30	chr4:74975800-74977800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:74975800-74978000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr4:74975800-74978600	Enhancers	HSMMtube	muscle
33	chr4:74975800-74980000	Enhancers	HMEC	breast
34	chr4:74975800-74980800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:74975800-74980800	Enhancers	Osteobl	bone
36	chr4:74975800-74981800	Weak transcription	Colon Smooth Muscle	Colon
37	chr4:74975800-74982600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:74976000-74977000	Weak transcription	Placenta	Placenta
39	chr4:74976000-74977000	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:74976000-74977400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr4:74976000-74977600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr4:74976000-74980200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr4:74976000-74982200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:74976000-74982600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr4:74976000-74984400	Enhancers	Hela-S3	cervix
46	chr4:74976200-74976800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr4:74976200-74977000	Weak transcription	Adipose Nuclei	Adipose
48	chr4:74976200-74977400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr4:74976200-74977400	Enhancers	NHLF	lung
50	chr4:74976200-74977600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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