Variant report

Variant	rs8181679
Chromosome Location	chr12:50611020-50611021
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50609830-50611657	K562	blood:	n/a	n/a
2	POLR2A	chr12:50610213-50611717	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50608910..50611527-chr12:50617767..50619869,3	MCF-7	breast:
2	chr12:50583119..50586019-chr12:50610359..50613018,3	K562	blood:
3	chr12:50583595..50586516-chr12:50609733..50613018,3	K562	blood:

Variant related genes	Relation type
ENSG00000257256	TF binding region
ENSG00000050405	Chromatin interaction
ENSG00000257298	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10219559	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1044370	0.90[ASW][hapmap];0.82[LWK][hapmap];0.83[YRI][hapmap]
rs10747573	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs10783342	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783343	0.86[AMR][1000 genomes]
rs1362984	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1862042	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2004283	0.95[AMR][1000 genomes]
rs2160994	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs2358538	0.89[ASW][hapmap];0.97[GIH][hapmap];0.80[MKK][hapmap];0.84[TSI][hapmap]
rs4459386	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580729	0.90[ASW][hapmap];0.82[LWK][hapmap];0.91[YRI][hapmap]
rs6580732	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6580734	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580738	0.88[LWK][hapmap]
rs7136648	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301566	0.84[EUR][1000 genomes]
rs7308356	0.91[YRI][hapmap]
rs7308692	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309519	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7957659	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9668955	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv975487	chr12:50610917-50612217	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs8181679	SLC4A8	cis	parietal	SCAN
rs8181679	DIP2B	cis	cerebellum	SCAN
rs8181679	LASS5	cis	parietal	SCAN
rs8181679	CERS5	cis	Nerve Tibial	GTEx
rs8181679	LASS5	cis	cerebellum	SCAN
rs8181679	SMARCD1	cis	cerebellum	SCAN
rs8181679	NELL2	cis	cerebellum	SCAN
rs8181679	LASS5	cis	multi-tissue	Pritchard
rs8181679	MCRS1	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
3	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
4	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:50591600-50615600	Weak transcription	HepG2	liver
7	chr12:50593400-50614200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:50593400-50614200	Weak transcription	Fetal Brain Male	brain
9	chr12:50593400-50614600	Weak transcription	Esophagus	oesophagus
10	chr12:50596200-50613400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:50596800-50614000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:50598400-50611400	Weak transcription	Spleen	Spleen
13	chr12:50598400-50613400	Weak transcription	K562	blood
14	chr12:50598600-50612400	Weak transcription	Psoas Muscle	Psoas
15	chr12:50598600-50613400	Weak transcription	Aorta	Aorta
16	chr12:50598600-50613400	Weak transcription	Fetal Kidney	kidney
17	chr12:50598600-50614000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr12:50598600-50614000	Weak transcription	Brain Germinal Matrix	brain
19	chr12:50599000-50612000	Weak transcription	Gastric	stomach
20	chr12:50599000-50614200	Weak transcription	Fetal Brain Female	brain
21	chr12:50599200-50614200	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:50599400-50614000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr12:50599400-50615000	Weak transcription	Liver	Liver
24	chr12:50599600-50613400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:50599600-50613400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:50599600-50614000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:50599600-50614000	Weak transcription	Brain Hippocampus Middle	brain
28	chr12:50599600-50614000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:50599800-50612400	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:50599800-50613400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:50599800-50613600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr12:50599800-50614000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr12:50599800-50614000	Weak transcription	Left Ventricle	heart
34	chr12:50599800-50614600	Weak transcription	Ovary	ovary
35	chr12:50599800-50635800	Weak transcription	Pancreas	Pancrea
36	chr12:50600000-50613400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:50600000-50613600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:50600000-50615800	Weak transcription	Lung	lung
39	chr12:50600200-50611200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr12:50600200-50613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:50600200-50614000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:50600200-50614200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr12:50600600-50614000	Weak transcription	Colonic Mucosa	Colon
44	chr12:50603200-50611400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:50603200-50612200	Weak transcription	Right Atrium	heart
46	chr12:50605600-50614200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:50605800-50614400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr12:50606200-50611400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:50606200-50612000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:50606200-50613400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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