Variant report

Variant	rs12131021
Chromosome Location	chr1:76081221-76081222
allele	C/G/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	POLR2A	chr1:76080391-76082524	H1-neurons	neurons:	n/a	n/a
2	UBTF	chr1:76081199-76081869	K562	blood:	n/a	n/a
3	CTBP2	chr1:76080347-76082590	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:76081220-76081370	HepG2	liver:	n/a	n/a
5	MXI1	chr1:76078645-76082977	SK-N-SH	brain:	n/a	chr1:76080753-76080768
6	POLR2A	chr1:76080399-76081446	H1-neurons	neurons:	n/a	n/a
7	SIN3A	chr1:76080355-76082876	H1-hESC	embryonic stem cell:	n/a	chr1:76082041-76082052 chr1:76081480-76081491 chr1:76082671-76082679
8	ELF1	chr1:76081143-76081543	GM12878	blood:	n/a	n/a
9	ZNF263	chr1:76080142-76082928	HEK293-T-REx	kidney:	n/a	chr1:76081515-76081524
10	GATA2	chr1:76080123-76081871	SH-SY5Y	brain:	n/a	n/a
11	REST	chr1:76080089-76083066	H1-neurons	neurons:	n/a	chr1:76081628-76081641 chr1:76082239-76082248 chr1:76082034-76082044 chr1:76082672-76082681 chr1:76080841-76080859 chr1:76081038-76081051 chr1:76080496-76080509
12	KAP1	chr1:76080079-76081236	HEK293	kidney:	n/a	n/a
13	CTCF	chr1:76081180-76081330	SK-N-SH_RA	brain:	n/a	n/a
14	CTCF	chr1:76079517-76082489	SK-N-SH	brain:	n/a	chr1:76082042-76082055

No.	Distal block	Cell Line	Cell type
1	chr1:76070009..76076148-chr1:76078248..76081967,7	K562	blood:
2	chr1:76071710..76074403-chr1:76079679..76081378,2	K562	blood:
3	chr1:76079907..76082887-chr11:62607623..62609125,2	K562	blood:
4	chr1:76080604..76083289-chr1:76094142..76096069,2	K562	blood:
5	chr1:76079906..76082887-chr11:62607618..62609123,2	K562	blood:
6	chr1:76080033..76082466-chr1:76250224..76251859,2	MCF-7	breast:
7	chr1:76079591..76081611-chr1:76189875..76191572,2	MCF-7	breast:
8	chr1:76066835..76069254-chr1:76079406..76081859,2	MCF-7	breast:
9	chr1:76079931..76081989-chr1:76083963..76086787,2	K562	blood:

Variant related genes	Relation type
SLC44A5	TF binding region
ENSG00000133316	Chromatin interaction
ENSG00000117054	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2057519	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4949869	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4949870	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6593584	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9324207	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv427675	chr1:76070382-76187748	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv10284	chr1:76079955-76082780	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12131021	MSH4	cis	Nerve Tibial	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76079400-76081400	Active TSS	Fetal Brain Male	brain
2	chr1:76079800-76082200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr1:76079800-76082600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr1:76080000-76081400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr1:76080000-76082000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:76080000-76082200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:76080000-76082400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr1:76080000-76082600	Active TSS	Brain Anterior Caudate	brain
9	chr1:76080000-76082800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
10	chr1:76080000-76082800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:76080200-76081400	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:76080200-76081400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
13	chr1:76080200-76081400	Bivalent Enhancer	Fetal Thymus	thymus
14	chr1:76080200-76081400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
15	chr1:76080200-76081400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
16	chr1:76080200-76081400	Flanking Bivalent TSS/Enh	Dnd41	blood
17	chr1:76080200-76081400	Flanking Active TSS	HUVEC	blood vessel
18	chr1:76080200-76081600	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
19	chr1:76080200-76081600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
20	chr1:76080200-76081800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:76080200-76081800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:76080200-76081800	Bivalent/Poised TSS	A549	lung
23	chr1:76080200-76082000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:76080200-76082200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:76080200-76082200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
26	chr1:76080200-76082400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:76080200-76082800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:76080200-76083000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
29	chr1:76080400-76081400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:76080400-76081400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
31	chr1:76080400-76081400	Bivalent/Poised TSS	Fetal Lung	lung
32	chr1:76080400-76081600	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
33	chr1:76080400-76081600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
34	chr1:76080400-76081600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
35	chr1:76080400-76081600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:76080400-76081600	Active TSS	Fetal Kidney	kidney
37	chr1:76080400-76081600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
38	chr1:76080400-76081800	Flanking Bivalent TSS/Enh	Colonic Mucosa	Colon
39	chr1:76080400-76082200	Active TSS	Brain Substantia Nigra	brain
40	chr1:76080400-76082400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
41	chr1:76080400-76082400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
42	chr1:76080400-76082600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr1:76080400-76082600	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:76080400-76082600	Active TSS	Aorta	Aorta
45	chr1:76080400-76082600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
46	chr1:76080400-76082800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr1:76080600-76081400	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:76080600-76081400	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:76080600-76081400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
50	chr1:76080600-76081400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose

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