Variant report

Variant	rs1800165
Chromosome Location	chr12:57591226-57591227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57590910-57591476	U87	brain:	n/a	n/a
2	POLR2A	chr12:57589540-57592773	U87	brain:	n/a	n/a
3	POLR2A	chr12:57590821-57591460	HepG2	liver:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57568829..57570904-chr12:57589670..57592502,2	MCF-7	breast:
2	chr12:57590967..57592740-chr12:57594355..57597058,2	K562	blood:
3	chr12:57400299..57402687-chr12:57590687..57592398,2	MCF-7	breast:
4	chr12:57503818..57506681-chr12:57589566..57591485,2	K562	blood:
5	chr12:57582255..57585186-chr12:57590822..57593487,2	MCF-7	breast:
6	chr12:57588577..57592670-chr12:57606671..57608811,3	K562	blood:
7	chr12:57585543..57587547-chr12:57591115..57593361,2	MCF-7	breast:

No data

Variant related genes	Relation type
LRP1	TF binding region
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10876967	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11172122	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1140648	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11837145	0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800139	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800154	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800156	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1800159	0.87[CEU][hapmap]
rs1800164	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1800166	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1800168	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800174	0.82[CHB][hapmap];0.85[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800175	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]
rs1800176	0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800177	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800180	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1800181	0.96[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1800182	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1800187	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800189	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800191	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1800194	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4074308	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4074309	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4077658	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6581125	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6581128	0.88[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7305179	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312323	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7398391	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7398426	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956957	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7965424	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7975818	0.96[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7978567	0.88[CEU][hapmap];0.83[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	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
8	esv1827238	chr12:57561918-57641094	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	esv1796377	chr12:57577246-57638936	Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	esv1809338	chr12:57580227-57628338	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	esv1827692	chr12:57582852-57651345	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
12	nsv519293	chr12:57583672-57637593	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	esv3388946	chr12:57588735-57591533	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv869636	chr12:57590172-57613714	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1800165	NPFF	cis	parietal	SCAN
rs1800165	OR6C1	cis	parietal	SCAN
rs1800165	KRT71	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57541600-57606600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:57541800-57607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:57547000-57606400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr12:57552800-57606800	Strong transcription	Fetal Intestine Large	intestine
5	chr12:57552800-57607000	Strong transcription	Liver	Liver
6	chr12:57553200-57607400	Strong transcription	Fetal Intestine Small	intestine
7	chr12:57557400-57606800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr12:57560800-57606200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:57560800-57606600	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:57565800-57606600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:57566000-57604200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:57566600-57606200	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:57569800-57600800	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr12:57570200-57606800	Strong transcription	Fetal Stomach	stomach
15	chr12:57570600-57606800	Strong transcription	Osteobl	bone
16	chr12:57570800-57605400	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr12:57576200-57605600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:57576200-57606400	Strong transcription	NHDF-Ad	bronchial
19	chr12:57576800-57604800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:57576800-57605000	Strong transcription	HSMMtube	muscle
21	chr12:57576800-57606600	Strong transcription	HepG2	liver
22	chr12:57576800-57607000	Strong transcription	Brain Germinal Matrix	brain
23	chr12:57577000-57591600	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr12:57577000-57600600	Strong transcription	Brain Cingulate Gyrus	brain
25	chr12:57577000-57600600	Strong transcription	Brain Substantia Nigra	brain
26	chr12:57577000-57606000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:57577000-57606400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr12:57577000-57606400	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr12:57577000-57606400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr12:57577000-57606600	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr12:57577000-57606800	Strong transcription	Colonic Mucosa	Colon
32	chr12:57577000-57606800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr12:57577000-57606800	Strong transcription	Ovary	ovary
34	chr12:57577200-57605800	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr12:57577200-57606000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:57577200-57606400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr12:57577200-57606400	Strong transcription	Aorta	Aorta
38	chr12:57577200-57606400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr12:57577200-57606400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr12:57577200-57606600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:57577200-57606800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr12:57577200-57606800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:57577200-57606800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr12:57577200-57606800	Weak transcription	A549	lung
45	chr12:57577400-57596200	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr12:57577400-57606600	Strong transcription	Esophagus	oesophagus
47	chr12:57577600-57606800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:57577600-57607200	Weak transcription	NHEK	skin
49	chr12:57578000-57593200	Strong transcription	NH-A	brain
50	chr12:57578800-57598400	Weak transcription	Thymus	Thymus

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