Variant report

Variant	rs2377138
Chromosome Location	chr5:118407683-118407684
allele	A/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	IRF1	chr5:118407516-118408591	K562	blood:	n/a	chr5:118408242-118408254 chr5:118407724-118407735 chr5:118408485-118408494 chr5:118407841-118407855 chr5:118408179-118408190 chr5:118407722-118407736 chr5:118408178-118408190 chr5:118408175-118408189 chr5:118408243-118408254 chr5:118407894-118407904 chr5:118407723-118407734 chr5:118408239-118408253
2	POLR2A	chr5:118405610-118407798	H1-hESC	embryonic stem cell:	n/a	n/a
3	BRCA1	chr5:118405866-118408029	Hela-S3	cervix:	n/a	chr5:118406754-118406763
4	HCFC1	chr5:118405625-118407889	Hela-S3	cervix:	n/a	n/a
5	IRF1	chr5:118407589-118407967	K562	blood:	n/a	chr5:118407724-118407735 chr5:118407841-118407855 chr5:118407722-118407736 chr5:118407894-118407904 chr5:118407723-118407734
6	REST	chr5:118405926-118407698	H1-neurons	neurons:	n/a	chr5:118407419-118407439 chr5:118406903-118406916 chr5:118406900-118406920 chr5:118406900-118406913 chr5:118407420-118407438
7	UBTF	chr5:118406105-118407793	K562	blood:	n/a	n/a
8	SIN3A	chr5:118406124-118407695	GM12878	blood:	n/a	chr5:118407111-118407122 chr5:118406900-118406913 chr5:118406400-118406414
9	MAZ	chr5:118405720-118407715	IMR90	lung:	n/a	chr5:118407061-118407071 chr5:118406183-118406196 chr5:118406185-118406194 chr5:118406184-118406195 chr5:118406187-118406194 chr5:118406183-118406196 chr5:118406183-118406191
10	BCLAF1	chr5:118406085-118407840	GM12878	blood:	n/a	chr5:118406362-118406375 chr5:118406895-118406908 chr5:118407174-118407183
11	POLR2A	chr5:118405743-118407783	MCF10A-Er-Src	breast:	n/a	n/a
12	SIN3A	chr5:118405880-118407827	H1-hESC	embryonic stem cell:	n/a	chr5:118407111-118407122 chr5:118406900-118406913 chr5:118406400-118406414
13	MTA3	chr5:118405723-118407710	GM12878	blood:	n/a	n/a
14	POLR2A	chr5:118405950-118407772	PBDE	blood:	n/a	n/a
15	CHD1	chr5:118407140-118407925	H1-hESC	embryonic stem cell:	n/a	n/a
16	MXI1	chr5:118405632-118408164	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:118323796..118326237-chr5:118405565..118407849,3	MCF-7	breast:
2	chr5:118406323..118408758-chr5:118602921..118606339,4	MCF-7	breast:
3	chr12:56435851..56438826-chr5:118405352..118408278,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239011	TF binding region
ENSG00000249494	TF binding region
ENSG00000145779	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000169570	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1375163	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17144918	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17144962	0.92[YRI][hapmap];1.00[AMR][1000 genomes]
rs17144994	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs1979092	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1979093	0.86[AFR][1000 genomes]
rs2135054	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2404394	0.91[YRI][hapmap];1.00[AMR][1000 genomes]
rs28581500	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2889564	1.00[AMR][1000 genomes]
rs36086810	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs36116741	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59926024	1.00[AMR][1000 genomes]
rs60051938	1.00[AMR][1000 genomes]
rs6867580	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6869894	0.89[AFR][1000 genomes]
rs6870423	0.86[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6870607	1.00[AMR][1000 genomes]
rs6870955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6871228	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6871822	0.96[AFR][1000 genomes]
rs6888039	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6889921	1.00[AMR][1000 genomes]
rs6893078	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72784072	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73244805	1.00[AMR][1000 genomes]
rs73247087	1.00[AMR][1000 genomes]
rs73247090	1.00[AMR][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	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv882774	chr5:118325429-118553470	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1018539	chr5:118355284-118445244	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118405200-118410000	Active TSS	K562	blood
2	chr5:118405400-118408000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:118405400-118408000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr5:118405400-118408200	Active TSS	A549	lung
5	chr5:118405400-118408200	Active TSS	HepG2	liver
6	chr5:118405400-118408400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr5:118405400-118408400	Active TSS	Hela-S3	cervix
8	chr5:118405400-118408600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr5:118405400-118409200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:118405600-118407800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:118405600-118407800	Active TSS	Colonic Mucosa	Colon
12	chr5:118405600-118407800	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr5:118405600-118408000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:118405600-118408000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:118405600-118408000	Active TSS	HSMM	muscle
16	chr5:118405600-118408400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr5:118405600-118408400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr5:118405600-118408400	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr5:118405600-118408400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr5:118405600-118409000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr5:118405600-118409200	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr5:118405600-118409200	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr5:118405600-118410000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr5:118405600-118410800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:118405800-118407800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr5:118405800-118407800	Active TSS	H9 Cell Line	embryonic stem cell
27	chr5:118405800-118407800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:118405800-118407800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:118405800-118407800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr5:118405800-118407800	Active TSS	Left Ventricle	heart
31	chr5:118405800-118407800	Active TSS	Right Ventricle	heart
32	chr5:118405800-118407800	Active TSS	Stomach Mucosa	stomach
33	chr5:118405800-118408000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:118405800-118408000	Active TSS	Muscle Satellite Cultured Cells	--
35	chr5:118405800-118408000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:118405800-118408000	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr5:118405800-118408000	Active TSS	Fetal Lung	lung
38	chr5:118405800-118408400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:118405800-118408400	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:118405800-118408400	Active TSS	Fetal Heart	heart
41	chr5:118405800-118408400	Active TSS	Thymus	Thymus
42	chr5:118405800-118408400	Active TSS	NHDF-Ad	bronchial
43	chr5:118405800-118408600	Active TSS	H1 Cell Line	embryonic stem cell
44	chr5:118405800-118408600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr5:118405800-118408800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr5:118405800-118408800	Active TSS	NHLF	lung
47	chr5:118405800-118409000	Active TSS	Brain Cingulate Gyrus	brain
48	chr5:118405800-118409000	Active TSS	Fetal Brain Female	brain
49	chr5:118405800-118409200	Active TSS	Fetal Kidney	kidney
50	chr5:118405800-118409200	Active TSS	Pancreatic Islets	Pancreatic Islet

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