Variant report

Variant	rs74147624
Chromosome Location	chr1:225842056-225842057
allele	A/G
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	MAZ	chr1:225839134-225842062	IMR90	lung:	n/a	chr1:225840253-225840263
2	CHD1	chr1:225842024-225842301	H1-hESC	embryonic stem cell:	n/a	n/a
3	STAT3	chr1:225841641-225842080	MCF10A-Er-Src	breast:	n/a	chr1:225841790-225841802
4	POLR2A	chr1:225841179-225842118	HepG2	liver:	n/a	n/a
5	REST	chr1:225841059-225842101	A549	lung:	n/a	chr1:225841262-225841275
6	POLR2A	chr1:225839665-225842385	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr1:225838660-225844042	MCF10A-Er-Src	breast:	n/a	n/a
8	YY1	chr1:225841354-225842374	SK-N-SH	brain:	n/a	chr1:225842133-225842145 chr1:225841471-225841485 chr1:225841789-225841798 chr1:225842135-225842145
9	POLR2A	chr1:225840071-225843898	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr1:225839159-225842396	HepG2	liver:	n/a	n/a
11	POLR2A	chr1:225840526-225842504	U87	brain:	n/a	n/a
12	POLR2A	chr1:225839363-225842398	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:225842029-225842078	MCF-7	breast:	n/a	n/a
14	ZNF263	chr1:225841172-225842286	HEK293-T-REx	kidney:	n/a	chr1:225841512-225841533 chr1:225841916-225841925
15	POLR2A	chr1:225840183-225842265	HUVEC	blood vessel:	n/a	n/a
16	YY1	chr1:225841920-225842309	SK-N-SH_RA	brain:	n/a	chr1:225842133-225842145 chr1:225842135-225842145
17	YY1	chr1:225841804-225842337	A549	lung:	n/a	chr1:225842133-225842145 chr1:225842135-225842145
18	CEBPB	chr1:225841470-225842164	A549	lung:	n/a	n/a
19	MAFK	chr1:225842048-225842196	H1-hESC	embryonic stem cell:	n/a	n/a
20	REST	chr1:225838932-225842208	H1-neurons	neurons:	n/a	chr1:225841262-225841275 chr1:225839877-225839885
21	YY1	chr1:225841954-225842293	H1-hESC	embryonic stem cell:	n/a	chr1:225842133-225842145 chr1:225842135-225842145
22	YY1	chr1:225841947-225842323	SK-N-SH_RA	brain:	n/a	chr1:225842133-225842145 chr1:225842135-225842145
23	JUND	chr1:225841185-225842293	H1-hESC	embryonic stem cell:	n/a	chr1:225841209-225841218
24	MAX	chr1:225839117-225842315	A549	lung:	n/a	chr1:225840253-225840263
25	MXI1	chr1:225838715-225842349	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:225840532-225842504	U87	brain:	n/a	n/a
27	MYC	chr1:225841426-225842172	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr1:225838940-225842419	MCF10A-Er-Src	breast:	n/a	n/a
29	POLR2A	chr1:225840277-225842282	HEK293	kidney:	n/a	n/a
30	POLR2A	chr1:225842036-225842346	U87	brain:	n/a	n/a
31	TCF12	chr1:225840479-225842348	A549	lung:	n/a	chr1:225841967-225841974

No.	Distal block	Cell Line	Cell type
1	chr1:225841590..225843627-chr1:225887293..225890031,4	MCF-7	breast:
2	chr1:225839962..225842492-chr1:226249684..226252539,2	MCF-7	breast:
3	chr1:225839775..225842863-chr1:225886341..225888955,3	MCF-7	breast:
4	chr1:225766054..225768167-chr1:225839556..225842131,2	MCF-7	breast:
5	chr1:225841158..225843185-chr1:226308432..226310542,2	MCF-7	breast:
6	chr1:225839309..225842570-chr1:226062972..226068660,6	MCF-7	breast:
7	chr1:225840996..225843850-chr1:225947438..225950251,2	MCF-7	breast:
8	chr1:225839340..225843768-chr1:225964006..225968066,9	MCF-7	breast:
9	chr1:225692749..225695160-chr1:225840876..225842568,2	MCF-7	breast:

Variant related genes	Relation type
ENAH	TF binding region
ENSG00000227496	Chromatin interaction
ENSG00000143742	Chromatin interaction
ENSG00000196187	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs55752939	1.00[AMR][1000 genomes]
rs56159213	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56396885	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56793390	0.96[AFR][1000 genomes]
rs74147610	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74147612	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74147616	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74147622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74147626	1.00[AMR][1000 genomes]
rs74147628	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	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	esv3435512	chr1:225838929-225842227	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
4	esv3329174	chr1:225839754-225842702	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225836600-225842200	Active TSS	Right Ventricle	heart
2	chr1:225836600-225842200	Active TSS	Stomach Smooth Muscle	stomach
3	chr1:225836800-225842200	Active TSS	NHLF	lung
4	chr1:225837000-225842800	Active TSS	Psoas Muscle	Psoas
5	chr1:225837200-225842800	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr1:225837400-225842200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr1:225837600-225842400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:225838000-225842200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:225838000-225842400	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:225838000-225842400	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr1:225838000-225842800	Active TSS	A549	lung
12	chr1:225838200-225842200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:225838200-225842200	Active TSS	HSMM	muscle
14	chr1:225838200-225842200	Active TSS	HSMMtube	muscle
15	chr1:225838200-225842400	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr1:225838200-225842400	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr1:225838200-225842400	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr1:225838200-225842800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:225838400-225842200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr1:225838400-225842200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:225838600-225842200	Active TSS	Fetal Muscle Trunk	muscle
22	chr1:225838800-225842200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr1:225838800-225842200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:225838800-225842200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:225838800-225842200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:225839000-225842200	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:225839200-225842200	Active TSS	Brain Angular Gyrus	brain
28	chr1:225839200-225842200	Active TSS	Brain Anterior Caudate	brain
29	chr1:225839200-225842200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:225839600-225842200	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr1:225839600-225842200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr1:225839600-225842200	Active TSS	Fetal Intestine Large	intestine
33	chr1:225840200-225842200	Active TSS	Rectal Mucosa Donor 29	rectum
34	chr1:225840600-225842200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:225840600-225842200	Active TSS	Colonic Mucosa	Colon
36	chr1:225841200-225842200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:225841400-225842200	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr1:225841400-225843000	Active TSS	Fetal Brain Male	brain
39	chr1:225841600-225842200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:225841600-225842200	Flanking Active TSS	Fetal Muscle Leg	muscle
41	chr1:225841600-225842200	Active TSS	Right Atrium	heart
42	chr1:225841600-225842200	Flanking Active TSS	HUVEC	blood vessel
43	chr1:225841800-225842200	Active TSS	Primary B cells from cord blood	blood
44	chr1:225841800-225842200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr1:225841800-225842200	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr1:225841800-225842200	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr1:225841800-225842400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:225841800-225842400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:225841800-225842400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:225841800-225842400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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