Variant report

Variant	rs7724372
Chromosome Location	chr5:102885995-102885996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:102882600..102886619-chr5:102891245..102894545,3	K562	blood:
2	chr5:102885075..102886971-chr5:102898644..102900760,2	K562	blood:
3	chr5:102880417..102882081-chr5:102883836..102886115,2	K562	blood:

Variant related genes	Relation type
ENSG00000112874	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10044216	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045774	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10057908	0.97[ASN][1000 genomes]
rs11750125	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11956617	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs159164	0.80[ASN][1000 genomes]
rs159165	0.80[ASN][1000 genomes]
rs159166	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs159167	0.83[ASN][1000 genomes]
rs159169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs169799	1.00[ASN][1000 genomes]
rs169800	1.00[ASN][1000 genomes]
rs1813569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1988929	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048150	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112340	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2401010	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs251162	0.80[ASN][1000 genomes]
rs251163	0.80[ASN][1000 genomes]
rs294041	0.99[ASN][1000 genomes]
rs294044	0.97[ASN][1000 genomes]
rs294045	1.00[ASN][1000 genomes]
rs294048	1.00[ASN][1000 genomes]
rs294098	0.95[ASN][1000 genomes]
rs3734087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs409474	0.93[ASN][1000 genomes]
rs443022	0.97[ASN][1000 genomes]
rs458304	0.95[ASN][1000 genomes]
rs4703253	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4703254	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6596534	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822416	1.00[ASN][1000 genomes]
rs822418	1.00[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	nsv882523	chr5:102687151-103342745	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1031600	chr5:102728430-103013575	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1025561	chr5:102744280-103152495	Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv537832	chr5:102744280-103152495	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1025859	chr5:102744479-103710290	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv537833	chr5:102744479-103710290	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7724372	FAM174A	cis	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:102874200-102897400	Weak transcription	Pancreas	Pancrea
2	chr5:102875400-102887800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:102875800-102897800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:102876600-102886000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr5:102876800-102887800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr5:102877000-102886000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:102877200-102888000	Weak transcription	Stomach Mucosa	stomach
8	chr5:102878400-102887800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr5:102878800-102886400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:102879800-102897200	Weak transcription	Brain Germinal Matrix	brain
11	chr5:102879800-102897400	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:102880200-102886600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr5:102880200-102886800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr5:102880200-102897200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:102880800-102886600	Weak transcription	Left Ventricle	heart
16	chr5:102881200-102897800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:102882200-102886800	Weak transcription	HSMM	muscle
18	chr5:102882400-102897400	Weak transcription	Psoas Muscle	Psoas
19	chr5:102882800-102897400	Weak transcription	Fetal Heart	heart
20	chr5:102882800-102897600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:102883000-102889200	Weak transcription	Colon Smooth Muscle	Colon
22	chr5:102883200-102897400	Weak transcription	GM12878-XiMat	blood
23	chr5:102884000-102886600	Weak transcription	Fetal Lung	lung
24	chr5:102884000-102891600	Weak transcription	Gastric	stomach
25	chr5:102884200-102886000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:102884200-102886000	Weak transcription	Fetal Kidney	kidney
27	chr5:102884200-102889200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:102884200-102894000	Weak transcription	NHEK	skin
29	chr5:102884400-102886000	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr5:102884400-102886200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr5:102884400-102886600	Weak transcription	Brain Anterior Caudate	brain
32	chr5:102884600-102886200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:102884600-102886400	Weak transcription	Fetal Intestine Large	intestine
34	chr5:102884600-102897400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr5:102884600-102897400	Weak transcription	HSMMtube	muscle
36	chr5:102884600-102897400	Weak transcription	NH-A	brain
37	chr5:102884600-102898000	Weak transcription	Small Intestine	intestine
38	chr5:102884800-102886400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:102884800-102886400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr5:102884800-102886400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr5:102884800-102886400	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:102884800-102886600	Weak transcription	Fetal Intestine Small	intestine
43	chr5:102884800-102887600	Weak transcription	NHDF-Ad	bronchial
44	chr5:102884800-102889200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:102884800-102893400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr5:102885000-102886600	Weak transcription	Brain Substantia Nigra	brain
47	chr5:102885000-102886600	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:102885000-102886600	Weak transcription	Fetal Muscle Leg	muscle
49	chr5:102885200-102886800	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr5:102885200-102886800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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