Variant report

Variant	rs12644791
Chromosome Location	chr4:7977611-7977612
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1317283	0.88[ASN][1000 genomes]
rs1317284	0.88[ASN][1000 genomes]
rs1317285	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1574393	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28447132	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28461913	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28480985	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28653042	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28712356	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4696724	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4696725	0.85[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes]
rs4696927	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4696930	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6818752	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6824006	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6830083	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7695963	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9685030	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491712	chr4:7582506-8155069	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv34140	chr4:7787936-8172491	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer 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
3	esv2754386	chr4:7822449-7992909	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2756298	chr4:7822449-7992909	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv829851	chr4:7958698-8049060	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv469779	chr4:7965253-8177646	Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv482448	chr4:7965253-8177646	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv878579	chr4:7969594-8011696	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	diseases
9	esv3325565	chr4:7976452-7980650	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12644791	MS4A1	trans	cerebellum	SCAN
rs12644791	CRMP1	cis	cerebellum	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7967000-7987600	Weak transcription	Psoas Muscle	Psoas
2	chr4:7970400-7980200	Weak transcription	HSMM	muscle
3	chr4:7972200-7979600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:7972200-7980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:7972400-7978400	Weak transcription	Fetal Kidney	kidney
6	chr4:7972400-7980200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr4:7973000-7978400	Weak transcription	Fetal Lung	lung
8	chr4:7973000-7980000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:7973000-7980200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr4:7973000-7980200	Weak transcription	Adipose Nuclei	Adipose
11	chr4:7973400-7978400	Weak transcription	Fetal Brain Male	brain
12	chr4:7973400-7978400	Weak transcription	Fetal Heart	heart
13	chr4:7973600-7980400	Weak transcription	Ovary	ovary
14	chr4:7974400-7979800	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:7974400-7989400	Weak transcription	Gastric	stomach
16	chr4:7974600-7978400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr4:7974600-7979600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr4:7974600-7979600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr4:7974600-7979800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:7974600-7979800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:7974600-7979800	Weak transcription	Colonic Mucosa	Colon
22	chr4:7974600-7979800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:7974600-7979800	Weak transcription	Fetal Stomach	stomach
24	chr4:7974600-7980000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:7974600-7980000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:7974600-7980000	Weak transcription	HUVEC	blood vessel
27	chr4:7974600-7980400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr4:7974800-7980200	Weak transcription	Lung	lung
29	chr4:7975000-7980400	Weak transcription	Pancreas	Pancrea
30	chr4:7975200-7978400	Weak transcription	Hela-S3	cervix
31	chr4:7975600-7978000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr4:7975600-7979000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr4:7975600-7979600	Weak transcription	Fetal Intestine Large	intestine
34	chr4:7975600-7979600	Weak transcription	HSMMtube	muscle
35	chr4:7975600-7979800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:7975600-7979800	Weak transcription	Esophagus	oesophagus
37	chr4:7975600-7979800	Weak transcription	Fetal Thymus	thymus
38	chr4:7975600-7980000	Weak transcription	Stomach Mucosa	stomach
39	chr4:7975600-7980000	Weak transcription	A549	lung
40	chr4:7975600-7983600	Weak transcription	Brain Angular Gyrus	brain
41	chr4:7975600-7984800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr4:7975800-7978000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr4:7975800-7978200	Weak transcription	Brain Anterior Caudate	brain
44	chr4:7975800-7979200	Weak transcription	Fetal Intestine Small	intestine
45	chr4:7975800-7979800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr4:7975800-7979800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr4:7975800-7979800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr4:7975800-7980000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:7975800-7980000	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr4:7975800-7980000	Weak transcription	NH-A	brain

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