Variant report

Variant	rs3845421
Chromosome Location	chr1:180988391-180988392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180987607..180995372-chr1:181053215..181062450,34	MCF-7	breast:
2	chr1:180977340..180979634-chr1:180986263..180988829,3	K562	blood:
3	chr1:180523368..180525230-chr1:180988182..180990982,2	K562	blood:
4	chr1:180987703..180989736-chr1:180991727..180994304,2	K562	blood:
5	chr1:180611289..180612983-chr1:180987142..180989197,2	K562	blood:
6	chr1:180987722..180989814-chr1:181005943..181007789,2	MCF-7	breast:
7	chr1:180977108..180979634-chr1:180985883..180988522,3	K562	blood:

Variant related genes	Relation type
ENSG00000162783	Chromatin interaction
ENSG00000272198	Chromatin interaction
ENSG00000135823	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10157092	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10159067	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10797661	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425660	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	esv3342865	chr1:180933678-181018012	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	esv3383831	chr1:180937224-181029755	Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv1011081	chr1:180973159-181135953	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	95 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	chr1:180940400-180988400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:180959200-180990800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:180973800-180989600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:180973800-180990600	Weak transcription	Colonic Mucosa	Colon
5	chr1:180973800-180990800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:180974000-180990800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:180974400-180990000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:180974600-180990000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:180974600-180990600	Weak transcription	Liver	Liver
10	chr1:180974600-180990600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:180974600-180990600	Weak transcription	Fetal Muscle Leg	muscle
12	chr1:180974800-180989800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:180974800-180990800	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:180975000-180989600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr1:180975000-180990000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr1:180975200-180990200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:180980000-180991000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:180980400-180990600	Weak transcription	Fetal Stomach	stomach
19	chr1:180980600-180989600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:180980800-180988600	Weak transcription	Fetal Brain Female	brain
21	chr1:180980800-180989400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr1:180980800-180989600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:180980800-180989800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:180980800-180990000	Weak transcription	Colon Smooth Muscle	Colon
25	chr1:180981000-180988400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr1:180981000-180990200	Weak transcription	NH-A	brain
27	chr1:180981000-180990600	Weak transcription	Stomach Smooth Muscle	stomach
28	chr1:180981200-180988600	Weak transcription	Hela-S3	cervix
29	chr1:180981200-180990400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:180981200-180991000	Weak transcription	Esophagus	oesophagus
31	chr1:180981400-180989600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:180981600-180989600	Weak transcription	Fetal Kidney	kidney
33	chr1:180981600-180989600	Weak transcription	Fetal Lung	lung
34	chr1:180981600-180989600	Weak transcription	HSMMtube	muscle
35	chr1:180981600-180990600	Weak transcription	Psoas Muscle	Psoas
36	chr1:180981600-180990600	Weak transcription	Right Atrium	heart
37	chr1:180981600-180990800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:180981800-180989600	Weak transcription	NHLF	lung
39	chr1:180982400-180989800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:180982800-180989600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:180982800-180991000	Weak transcription	Pancreas	Pancrea
42	chr1:180983000-180989400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:180983000-180990000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:180983000-180991200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:180984200-180990400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr1:180984200-180990600	Weak transcription	Aorta	Aorta
47	chr1:180984400-180990000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:180984400-180990200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:180984400-180990800	Weak transcription	Ovary	ovary
50	chr1:180984400-180990800	Weak transcription	Small Intestine	intestine

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