Variant report

Variant	rs6580736
Chromosome Location	chr12:50679418-50679419
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:50677350..50679861-chr12:50792501..50795030,2	K562	blood:
2	chr12:50593299..50595374-chr12:50677220..50679734,2	K562	blood:
3	chr12:50678651..50681144-chr12:50681801..50683529,3	K562	blood:
4	chr12:50676871..50679447-chr12:50689934..50691681,2	K562	blood:
5	chr12:50614322..50618314-chr12:50675052..50679891,5	K562	blood:
6	chr12:50614024..50616982-chr12:50677879..50679870,2	K562	blood:
7	chr12:50504614..50508392-chr12:50676689..50680044,5	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LARP4-5	chr12:50679362-50680433	NONHSAT028192

No data

Variant related genes	Relation type
ENSG00000178449	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000161813	Chromatin interaction
ENSG00000272368	Chromatin interaction
ENSG00000269529	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10506292	0.96[CEU][hapmap]
rs10783344	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs10783349	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783350	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876013	0.86[EUR][1000 genomes]
rs10876014	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10876015	0.96[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs10876016	0.93[EUR][1000 genomes]
rs10876017	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs10876018	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876023	0.96[CEU][hapmap]
rs10876024	0.96[CEU][hapmap]
rs10876027	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169314	0.83[EUR][1000 genomes]
rs11169315	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs11169317	0.85[EUR][1000 genomes]
rs11169319	0.82[EUR][1000 genomes]
rs11169322	0.96[CEU][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169331	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs11169332	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169335	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs11169339	0.88[EUR][1000 genomes]
rs11169345	0.92[EUR][1000 genomes]
rs11169347	0.92[EUR][1000 genomes]
rs11169348	0.96[CEU][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs11169349	0.93[EUR][1000 genomes]
rs11169350	0.96[CEU][hapmap];0.93[EUR][1000 genomes]
rs11169351	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11169357	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11169359	0.92[EUR][1000 genomes]
rs11169360	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs11169367	0.89[EUR][1000 genomes]
rs11169369	0.93[EUR][1000 genomes]
rs11169370	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11169371	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169373	0.91[EUR][1000 genomes]
rs11169374	0.91[EUR][1000 genomes]
rs11169375	0.89[EUR][1000 genomes]
rs11169376	0.88[EUR][1000 genomes]
rs11169377	0.88[EUR][1000 genomes]
rs11169379	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169386	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11833608	0.88[CEU][hapmap];0.91[TSI][hapmap]
rs11836169	0.89[EUR][1000 genomes]
rs11838347	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs12303082	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs12367872	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs12422417	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs12424691	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12424713	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs12425229	0.86[EUR][1000 genomes]
rs12425705	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs12426444	0.84[EUR][1000 genomes]
rs12811291	0.86[EUR][1000 genomes]
rs12821454	0.92[EUR][1000 genomes]
rs12821504	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12823506	0.88[EUR][1000 genomes]
rs12828340	0.96[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs12832940	0.92[EUR][1000 genomes]
rs1362983	0.96[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs17124562	0.86[EUR][1000 genomes]
rs1972611	0.88[EUR][1000 genomes]
rs2111988	0.96[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2302900	0.92[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2358539	0.96[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs28628775	0.92[EUR][1000 genomes]
rs34039674	0.88[EUR][1000 genomes]
rs34614542	0.89[EUR][1000 genomes]
rs34825838	0.84[EUR][1000 genomes]
rs34849043	0.90[EUR][1000 genomes]
rs34858415	0.89[EUR][1000 genomes]
rs35209607	0.91[EUR][1000 genomes]
rs35535298	0.91[EUR][1000 genomes]
rs35663729	0.85[EUR][1000 genomes]
rs35768991	0.87[EUR][1000 genomes]
rs35878271	0.88[EUR][1000 genomes]
rs35933908	0.93[EUR][1000 genomes]
rs3812825	0.96[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs3861100	0.84[EUR][1000 genomes]
rs4348979	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs4421818	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs4768872	0.88[EUR][1000 genomes]
rs4768891	0.82[AFR][1000 genomes]
rs4768928	0.91[YRI][hapmap]
rs4768949	0.88[EUR][1000 genomes]
rs4768951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6580735	0.92[EUR][1000 genomes]
rs6580737	0.93[EUR][1000 genomes]
rs6580738	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580739	0.89[EUR][1000 genomes]
rs6580740	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580741	0.88[EUR][1000 genomes]
rs67138019	0.91[EUR][1000 genomes]
rs7132551	0.96[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7134595	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7135777	0.92[EUR][1000 genomes]
rs7138420	0.92[CEU][hapmap]
rs7138622	0.92[CEU][hapmap]
rs71465002	0.86[EUR][1000 genomes]
rs7296291	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7301186	0.83[EUR][1000 genomes]
rs7301189	0.82[EUR][1000 genomes]
rs7304445	0.92[EUR][1000 genomes]
rs7305995	0.92[EUR][1000 genomes]
rs7308095	0.83[EUR][1000 genomes]
rs7308885	0.86[EUR][1000 genomes]
rs7310541	0.89[EUR][1000 genomes]
rs7311378	0.92[EUR][1000 genomes]
rs7311491	0.92[EUR][1000 genomes]
rs7311973	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs7312252	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs7314465	0.86[EUR][1000 genomes]
rs7315690	0.92[CEU][hapmap]
rs7315871	0.86[EUR][1000 genomes]
rs7315955	0.87[EUR][1000 genomes]
rs7399343	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7485486	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7486747	0.96[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs7488682	0.93[EUR][1000 genomes]
rs7489214	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7953953	0.96[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7956468	0.93[EUR][1000 genomes]
rs7957659	0.87[LWK][hapmap]
rs7974648	0.87[EUR][1000 genomes]
rs7979830	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7980911	0.92[EUR][1000 genomes]
rs9705460	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv702	chr12:50670870-50715934	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6580736	KIAA1463	cis	multi-tissue	Pritchard
rs6580736	CELA1	cis	parietal	SCAN
rs6580736	SLC38A1	cis	parietal	SCAN
rs6580736	CERS5	cis	Nerve Tibial	GTEx
rs6580736	LASS5	cis	cerebellum	SCAN
rs6580736	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs6580736	MCRS1	cis	parietal	SCAN
rs6580736	LASS5	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50678000-50680000	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr12:50678000-50680600	Enhancers	Stomach Mucosa	stomach
3	chr12:50678000-50684400	Weak transcription	Esophagus	oesophagus
4	chr12:50678000-50691600	Weak transcription	Gastric	stomach
5	chr12:50678000-50699800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:50678400-50679600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr12:50678400-50679600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr12:50678400-50679600	Enhancers	Dnd41	blood
9	chr12:50678400-50679600	Enhancers	NHEK	skin
10	chr12:50678400-50680000	Enhancers	HepG2	liver
11	chr12:50678400-50680600	Weak transcription	Brain Substantia Nigra	brain
12	chr12:50678400-50681800	Weak transcription	Fetal Lung	lung
13	chr12:50678400-50685600	Weak transcription	Primary T cells from cord blood	blood
14	chr12:50678400-50686800	Weak transcription	HSMMtube	muscle
15	chr12:50678400-50689600	Weak transcription	Ovary	ovary
16	chr12:50678400-50690800	Weak transcription	Fetal Stomach	stomach
17	chr12:50678400-50690800	Weak transcription	A549	lung
18	chr12:50678400-50691000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:50678400-50696000	Weak transcription	HSMM	muscle
20	chr12:50678400-50708600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:50678600-50679800	Enhancers	Liver	Liver
22	chr12:50678600-50680800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr12:50678600-50680800	Weak transcription	Spleen	Spleen
24	chr12:50678600-50691800	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:50678600-50695600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr12:50678600-50698800	Weak transcription	Pancreas	Pancrea
27	chr12:50678800-50679600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr12:50678800-50679800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:50678800-50681800	Weak transcription	Right Atrium	heart
30	chr12:50678800-50682000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:50678800-50690600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:50678800-50691200	Weak transcription	Left Ventricle	heart
33	chr12:50678800-50691600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:50679000-50679600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:50679000-50679600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr12:50679000-50679800	Weak transcription	Small Intestine	intestine
37	chr12:50679000-50680000	Enhancers	K562	blood
38	chr12:50679000-50682000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:50679000-50684600	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:50679000-50696200	Weak transcription	Osteobl	bone
41	chr12:50679200-50679600	Enhancers	GM12878-XiMat	blood
42	chr12:50679200-50679800	Enhancers	Duodenum Mucosa	Duodenum

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