Variant report

Variant	rs1800175
Chromosome Location	chr12:57561379-57561380
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57520220..57523882-chr12:57558135..57563846,11	MCF-7	breast:
2	chr12:57470985..57473736-chr12:57560913..57563302,2	K562	blood:
3	chr12:57480714..57483772-chr12:57558111..57562184,3	MCF-7	breast:
4	chr12:57520113..57524524-chr12:57557752..57564598,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166886	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10876967	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172122	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1140648	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11837145	0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1800139	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800154	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800156	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1800164	0.84[JPT][hapmap]
rs1800165	0.91[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800166	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1800168	0.91[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800174	0.89[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800176	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1800177	0.94[CHB][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800180	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800181	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800182	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800187	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800189	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800191	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800194	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4074308	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4074309	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4077658	0.81[AMR][1000 genomes]
rs6581125	0.96[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6581128	0.89[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7305179	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7312323	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7398391	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7398426	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7956957	0.84[JPT][hapmap]
rs7975818	0.96[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7978567	0.80[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	nsv559023	chr12:57530670-57616061	Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv518980	chr12:57532982-57637593	Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv899112	chr12:57535266-57601388	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
5	nsv525873	chr12:57535266-57616013	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv899113	chr12:57543572-57601388	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	12 gene(s)	inside rSNPs	diseases
7	nsv899114	chr12:57556768-57587839	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	esv1810281	chr12:57558657-57641094	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1800175	KRT71	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57531800-57576000	Strong transcription	Fetal Brain Female	brain
2	chr12:57540600-57569400	Strong transcription	Brain Germinal Matrix	brain
3	chr12:57541600-57606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:57541800-57607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr12:57542200-57565600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:57546600-57565200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:57547000-57565200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr12:57547000-57575600	Strong transcription	H1 Cell Line	embryonic stem cell
9	chr12:57547000-57575600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr12:57547000-57606400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr12:57547200-57562400	Weak transcription	Small Intestine	intestine
12	chr12:57547400-57567400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:57547400-57575400	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr12:57547600-57575400	Strong transcription	Cortex derived primary cultured neurospheres	brain
15	chr12:57547600-57575600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:57547800-57565000	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr12:57547800-57565200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr12:57547800-57565400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr12:57548400-57561600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:57549000-57562400	Weak transcription	GM12878-XiMat	blood
21	chr12:57549000-57575200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:57552600-57563800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:57552600-57565000	Strong transcription	Fetal Stomach	stomach
24	chr12:57552800-57562400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr12:57552800-57563000	Strong transcription	Ovary	ovary
26	chr12:57552800-57564200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:57552800-57566800	Weak transcription	Right Atrium	heart
28	chr12:57552800-57568400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:57552800-57575200	Strong transcription	Duodenum Mucosa	Duodenum
30	chr12:57552800-57606800	Strong transcription	Fetal Intestine Large	intestine
31	chr12:57552800-57607000	Strong transcription	Liver	Liver
32	chr12:57553000-57562600	Strong transcription	Brain Cingulate Gyrus	brain
33	chr12:57553000-57565000	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:57553200-57607400	Strong transcription	Fetal Intestine Small	intestine
35	chr12:57553600-57564600	Strong transcription	Stomach Smooth Muscle	stomach
36	chr12:57553600-57565200	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr12:57553800-57563600	Strong transcription	Fetal Muscle Leg	muscle
38	chr12:57553800-57564600	Strong transcription	Colon Smooth Muscle	Colon
39	chr12:57554200-57563200	Strong transcription	Fetal Muscle Trunk	muscle
40	chr12:57554400-57568800	Strong transcription	Brain Hippocampus Middle	brain
41	chr12:57555400-57583200	Weak transcription	Fetal Heart	heart
42	chr12:57556800-57564600	Strong transcription	Adipose Nuclei	Adipose
43	chr12:57557000-57565000	Strong transcription	Placenta	Placenta
44	chr12:57557400-57606800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr12:57558000-57561400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:57558000-57561400	Genic enhancers	HSMM	muscle
47	chr12:57558000-57561400	Genic enhancers	NHDF-Ad	bronchial
48	chr12:57558000-57562400	Strong transcription	Fetal Kidney	kidney
49	chr12:57558000-57563800	Strong transcription	Colonic Mucosa	Colon
50	chr12:57558000-57565200	Strong transcription	Fetal Lung	lung

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