Variant report

Variant	rs1472275
Chromosome Location	chr1:247054530-247054531
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247017312..247021045-chr1:247051011..247055284,3	K562	blood:
2	chr1:247041147..247045524-chr1:247051435..247055344,4	K562	blood:
3	chr1:247053838..247055850-chr1:247057759..247060432,2	K562	blood:
4	chr1:247053879..247054578-chr11:118965786..118966471,2	NB4	blood:

Variant related genes	Relation type
ENSG00000188486	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1039009	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1039010	0.80[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11579381	0.95[JPT][hapmap]
rs11585741	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1612610	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613209	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1619941	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1691240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691241	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691242	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1691252	0.86[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1691254	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691255	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779964	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779968	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779969	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172796	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2642975	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2642977	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2642990	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2642991	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800214	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2800215	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800219	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800220	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2800221	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2818888	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971278	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs7542895	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs768197	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs903461	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs9729306	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9729316	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2762192	chr1:246823857-247069232	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	nsv1011346	chr1:246868799-247133898	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv1810844	chr1:246988018-247054824	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv5276	chr1:247028364-247073098	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
10	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1472275	AHCTF1	cis	Esophagus Muscularis	GTEx
rs1472275	ZNF124	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247002200-247082400	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:247002400-247081000	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr1:247004200-247083400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:247005200-247079800	Weak transcription	Stomach Mucosa	stomach
5	chr1:247006600-247071600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:247018400-247056400	Weak transcription	Fetal Heart	heart
7	chr1:247020400-247072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:247031600-247071400	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:247033200-247060800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:247033600-247058000	Weak transcription	Colonic Mucosa	Colon
11	chr1:247033800-247070800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:247039000-247057200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:247039000-247070400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:247040400-247065000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:247043200-247057200	Weak transcription	Fetal Intestine Small	intestine
16	chr1:247043800-247082000	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:247044800-247070200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:247045400-247082600	Strong transcription	Dnd41	blood
19	chr1:247045600-247070800	Strong transcription	Primary hematopoietic stem cells	blood
20	chr1:247045600-247071000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:247045600-247071000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr1:247045800-247070600	Strong transcription	Liver	Liver
23	chr1:247045800-247070800	Strong transcription	Osteobl	bone
24	chr1:247045800-247071000	Strong transcription	Adipose Nuclei	Adipose
25	chr1:247045800-247071000	Strong transcription	K562	blood
26	chr1:247045800-247071200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr1:247045800-247071600	Strong transcription	HSMM	muscle
28	chr1:247045800-247072000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr1:247045800-247080200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:247045800-247082400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:247045800-247083400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:247046000-247055200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr1:247046000-247055200	Strong transcription	HUVEC	blood vessel
34	chr1:247046000-247055200	Strong transcription	NH-A	brain
35	chr1:247046000-247055600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:247046000-247055600	Strong transcription	Primary B cells from cord blood	blood
37	chr1:247046000-247070800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:247046000-247070800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:247046000-247071000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:247046000-247071200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:247046000-247081400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:247046000-247082000	Strong transcription	Fetal Thymus	thymus
43	chr1:247046000-247082800	Strong transcription	Hela-S3	cervix
44	chr1:247046200-247071600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr1:247046200-247081200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:247046200-247081400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr1:247046200-247081400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr1:247047600-247055400	Strong transcription	Placenta	Placenta
49	chr1:247047800-247070200	Strong transcription	HepG2	liver
50	chr1:247048000-247055000	Strong transcription	NHDF-Ad	bronchial

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