Variant report

Variant	rs1371799
Chromosome Location	chr4:74977837-74977838
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	STAT3	chr4:74977710-74977994	MCF10A-Er-Src	breast:	n/a	n/a
2	CTCF	chr4:74977820-74977970	RPTEC	kidney:	n/a	n/a
3	CTCF	chr4:74977820-74977970	NHEK	skin:	n/a	n/a
4	FOS	chr4:74977690-74978067	MCF10A-Er-Src	breast:	n/a	n/a
5	MAX	chr4:74977768-74978605	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr4:74977589-74978072	MCF10A-Er-Src	breast:	n/a	n/a
7	EP300	chr4:74977496-74978258	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr4:74977195-74978407	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF12	chr4:74977564-74978709	ECC-1	luminal epithelium:	n/a	n/a
10	MYC	chr4:74977692-74978084	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr4:74977638-74978044	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr4:74977683-74978045	MCF10A-Er-Src	breast:	n/a	n/a
13	MYC	chr4:74977701-74978101	MCF10A-Er-Src	breast:	n/a	n/a
14	FOS	chr4:74977693-74978009	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr4:74977699-74977989	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr4:74977693-74978001	MCF10A-Er-Src	breast:	n/a	n/a

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	chr4:74975738..74977942-chr4:74982143..74984309,2	K562	blood:

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

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13128896	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1371794	0.81[EUR][1000 genomes]
rs1371798	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];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4121652	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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];0.96[ASN][1000 genomes]
rs7684973	0.82[JPT][hapmap]
rs7686861	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs882638	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs981458	0.90[EUR][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	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
5	esv3379316	chr4:74977405-74978942	Weak transcription Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
White blood cell count	21738479	GWAS catalog

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74966800-74978000	Weak transcription	Gastric	stomach
2	chr4:74972000-74982000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr4:74972200-74978000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr4:74972800-74980200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:74973000-74978600	Enhancers	HUVEC	blood vessel
6	chr4:74973400-74980200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:74974200-74981000	Enhancers	Placenta Amnion	Placenta Amnion
8	chr4:74974400-74978000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr4:74974600-74978000	Weak transcription	Brain Hippocampus Middle	brain
10	chr4:74975400-74978000	Weak transcription	Aorta	Aorta
11	chr4:74975600-74978000	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:74975600-74978000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:74975600-74978000	Weak transcription	Pancreas	Pancrea
14	chr4:74975600-74980000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr4:74975600-74980800	Enhancers	NHDF-Ad	bronchial
16	chr4:74975800-74978000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr4:74975800-74978600	Enhancers	HSMMtube	muscle
18	chr4:74975800-74980000	Enhancers	HMEC	breast
19	chr4:74975800-74980800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr4:74975800-74980800	Enhancers	Osteobl	bone
21	chr4:74975800-74981800	Weak transcription	Colon Smooth Muscle	Colon
22	chr4:74975800-74982600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:74976000-74980200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:74976000-74982200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:74976000-74982600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr4:74976000-74984400	Enhancers	Hela-S3	cervix
27	chr4:74976200-74979000	Enhancers	NH-A	brain
28	chr4:74976600-74978400	Enhancers	A549	lung
29	chr4:74976600-74978600	Enhancers	HSMM	muscle
30	chr4:74976600-74978800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:74976600-74979200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:74976600-74979600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr4:74976600-74980800	Enhancers	Muscle Satellite Cultured Cells	--
34	chr4:74977000-74978400	Enhancers	Adipose Nuclei	Adipose
35	chr4:74977000-74978400	Enhancers	Left Ventricle	heart
36	chr4:74977000-74978400	Enhancers	Stomach Mucosa	stomach
37	chr4:74977000-74980800	Enhancers	Placenta	Placenta
38	chr4:74977200-74981000	Weak transcription	Liver	Liver
39	chr4:74977200-74982200	Weak transcription	Fetal Intestine Small	intestine
40	chr4:74977200-74983000	Weak transcription	Fetal Intestine Large	intestine
41	chr4:74977400-74978200	Enhancers	Fetal Muscle Leg	muscle
42	chr4:74977400-74978200	Enhancers	Right Ventricle	heart
43	chr4:74977400-74978400	Enhancers	Esophagus	oesophagus
44	chr4:74977400-74978400	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr4:74977400-74978400	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr4:74977400-74978400	Flanking Active TSS	NHEK	skin
47	chr4:74977400-74978600	Enhancers	Rectal Mucosa Donor 31	rectum
48	chr4:74977400-74980600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:74977400-74982400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:74977600-74978200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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