Variant report

Variant	rs2800221
Chromosome Location	chr1:247058705-247058706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247053838..247055850-chr1:247057759..247060432,2	K562	blood:
2	chr1:247056860..247058918-chr1:247092602..247094534,2	MCF-7	breast:
3	chr1:247058694..247061566-chr1:247068507..247070182,2	K562	blood:
4	chr1:247056985..247059643-chr1:247065954..247067972,2	K562	blood:
5	chr1:247029799..247031525-chr1:247058523..247060785,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1039009	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1039010	1.00[ASW][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11579381	0.91[JPT][hapmap]
rs11585741	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1472275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612610	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1613209	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1619941	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1691240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691241	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691242	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1691252	1.00[ASW][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1691254	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1691255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1779968	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1779969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2172796	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2642975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2642977	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.81[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2642990	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2642991	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2800214	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2800215	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2800219	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800220	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2818888	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971278	0.81[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs7542895	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs768197	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs903461	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9729306	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9729316	0.88[EUR][1000 genomes];0.92[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	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	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
7	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
8	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
9	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2800221	ZNF124	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr1:247020400-247072800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:247031600-247071400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr1:247033200-247060800	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:247033800-247070800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:247039000-247070400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:247040400-247065000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:247043800-247082000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:247044800-247070200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:247045400-247082600	Strong transcription	Dnd41	blood
15	chr1:247045600-247070800	Strong transcription	Primary hematopoietic stem cells	blood
16	chr1:247045600-247071000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:247045600-247071000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:247045800-247070600	Strong transcription	Liver	Liver
19	chr1:247045800-247070800	Strong transcription	Osteobl	bone
20	chr1:247045800-247071000	Strong transcription	Adipose Nuclei	Adipose
21	chr1:247045800-247071000	Strong transcription	K562	blood
22	chr1:247045800-247071200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:247045800-247071600	Strong transcription	HSMM	muscle
24	chr1:247045800-247072000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:247045800-247080200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr1:247045800-247082400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:247045800-247083400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:247046000-247070800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr1:247046000-247070800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr1:247046000-247071000	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:247046000-247071200	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:247046000-247081400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:247046000-247082000	Strong transcription	Fetal Thymus	thymus
34	chr1:247046000-247082800	Strong transcription	Hela-S3	cervix
35	chr1:247046200-247071600	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:247046200-247081200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:247046200-247081400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr1:247046200-247081400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:247047800-247070200	Strong transcription	HepG2	liver
40	chr1:247048200-247070400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:247048800-247059400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:247049600-247060800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:247049600-247070600	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr1:247049800-247063000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:247052400-247060400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr1:247052400-247060400	Weak transcription	Aorta	Aorta
47	chr1:247052400-247062200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:247052800-247058800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:247053000-247060400	Weak transcription	Gastric	stomach
50	chr1:247053000-247060800	Weak transcription	Spleen	Spleen

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