Variant report

Variant	rs6581128
Chromosome Location	chr12:57583672-57583673
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:57583280-57584377	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:57582883-57585896	U87	brain:	n/a	n/a
3	POLR2A	chr12:57583338-57583742	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:57583608-57583855	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:57582803-57586073	U87	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57502051..57503963-chr12:57583125..57585468,2	K562	blood:
2	chr12:57581983..57583861-chr12:57587969..57590424,2	K562	blood:
3	chr12:57582255..57585186-chr12:57590822..57593487,2	MCF-7	breast:
4	chr12:57580575..57582415-chr12:57582574..57584680,3	MCF-7	breast:

No data

Variant related genes	Relation type
MIR1228	TF binding region
ENSG00000166888	Chromatin interaction
ENSG00000123384	Chromatin interaction
ENSG00000221365	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10876967	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172122	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1140648	0.96[CEU][hapmap];0.87[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];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11837145	0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1800139	0.92[CEU][hapmap];0.91[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];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1800154	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800156	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1800164	0.85[JPT][hapmap]
rs1800165	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]
rs1800166	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1800168	0.88[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1800174	1.00[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800175	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]
rs1800176	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1800177	0.89[CHB][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800180	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1800181	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1800182	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1800187	0.92[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1800189	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1800191	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1800194	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4074308	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4074309	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4077658	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6581125	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7305179	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7312323	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398391	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7398426	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7956957	0.84[JPT][hapmap]
rs7975818	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7978567	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	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
9	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
10	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
11	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
12	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
13	esv3361030	chr12:57583385-57587783	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6581128	LRP1	cis	brain	BrainEAC
rs6581128	LRP1	cis	cerebellar cortex	BrainEAC
rs6581128	TIMELESS	cis	cerebellum	SCAN
rs6581128	KRT71	cis	parietal	SCAN
rs6581128	LRP1	cis	frontal cortex	BrainEAC
rs6581128	LRP1	cis	hippocampus	BrainEAC
rs6581128	LRP1	cis	occipital cortex	BrainEAC

Chromatin state (count:99 , 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	chr12:57567400-57584200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr12:57569400-57584000	Strong transcription	Rectal Smooth Muscle	rectum
15	chr12:57569800-57600800	Strong transcription	Brain Inferior Temporal Lobe	brain
16	chr12:57570200-57606800	Strong transcription	Fetal Stomach	stomach
17	chr12:57570600-57606800	Strong transcription	Osteobl	bone
18	chr12:57570800-57605400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr12:57571000-57585200	Weak transcription	Fetal Brain Male	brain
20	chr12:57574400-57586400	Weak transcription	Small Intestine	intestine
21	chr12:57574600-57584400	Genic enhancers	Placenta	Placenta
22	chr12:57575600-57585400	Strong transcription	NHLF	lung
23	chr12:57575800-57583800	Strong transcription	Fetal Lung	lung
24	chr12:57576000-57586400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr12:57576200-57583800	Strong transcription	Adipose Nuclei	Adipose
26	chr12:57576200-57605600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:57576200-57606400	Strong transcription	NHDF-Ad	bronchial
28	chr12:57576600-57583800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:57576800-57583800	Strong transcription	Fetal Brain Female	brain
30	chr12:57576800-57583800	Strong transcription	Right Ventricle	heart
31	chr12:57576800-57584000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:57576800-57604800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:57576800-57605000	Strong transcription	HSMMtube	muscle
34	chr12:57576800-57606600	Strong transcription	HepG2	liver
35	chr12:57576800-57607000	Strong transcription	Brain Germinal Matrix	brain
36	chr12:57577000-57583800	Strong transcription	Brain Hippocampus Middle	brain
37	chr12:57577000-57585200	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr12:57577000-57585400	Strong transcription	Gastric	stomach
39	chr12:57577000-57585800	Strong transcription	Spleen	Spleen
40	chr12:57577000-57591600	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr12:57577000-57600600	Strong transcription	Brain Cingulate Gyrus	brain
42	chr12:57577000-57600600	Strong transcription	Brain Substantia Nigra	brain
43	chr12:57577000-57606000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:57577000-57606400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr12:57577000-57606400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:57577000-57606400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr12:57577000-57606600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr12:57577000-57606800	Strong transcription	Colonic Mucosa	Colon
49	chr12:57577000-57606800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr12:57577000-57606800	Strong transcription	Ovary	ovary

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