Variant report

Variant	rs7504908
Chromosome Location	chr18:12327670-12327671
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12326610..12329531-chr18:12345166..12347702,2	MCF-7	breast:
2	chr18:12327453..12330082-chr18:12330908..12334376,4	K562	blood:
3	chr18:12306580..12311152-chr18:12324883..12329594,7	K562	blood:
4	chr18:12327171..12330634-chr18:12335563..12338039,3	K562	blood:
5	chr18:12306391..12309580-chr18:12325150..12328267,3	MCF-7	breast:
6	chr18:12321262..12324555-chr18:12324806..12328664,5	K562	blood:
7	chr18:12326926..12330027-chr18:12336658..12338929,3	MCF-7	breast:
8	chr18:12326777..12329132-chr18:12461073..12463843,2	K562	blood:
9	chr18:12327453..12329462-chr18:12331955..12334376,2	K562	blood:
10	chr18:12311936..12317885-chr18:12323414..12329476,8	K562	blood:
11	chr18:12326916..12328882-chr18:12376768..12379583,2	K562	blood:
12	chr18:12270234..12271756-chr18:12327004..12329574,2	MCF-7	breast:
13	chr18:12326458..12332320-chr18:12374113..12378268,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10459999	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10460000	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10460001	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10853225	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11080564	0.95[CEU][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11080565	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11080569	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11080571	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11080572	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1129115	1.00[CEU][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11553521	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11662523	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11664216	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11665134	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11875938	0.86[EUR][1000 genomes]
rs12455273	0.86[EUR][1000 genomes]
rs12456857	0.95[CEU][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12604732	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12954686	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12968089	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12968566	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1941222	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2298542	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs2298543	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs28372882	0.87[EUR][1000 genomes]
rs34829762	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35338639	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3786260	0.85[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs478088	0.85[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.88[TSI][hapmap]
rs4796961	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4796964	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4797677	0.95[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4797680	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs62098961	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7231182	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7231409	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7235237	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7235296	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7407640	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7504974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7505626	0.86[LWK][hapmap]
rs7505834	0.95[CEU][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8086821	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8086993	0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8087840	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8092506	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8093375	0.81[CEU][hapmap]
rs8097342	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs9303769	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9303770	0.85[CEU][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs9946698	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9951945	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9956171	0.85[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1061545	chr18:12235999-12328405	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
7	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
8	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7504908	TUBB6	cis	Whole Blood	GTEx
rs7504908	TUBB6	cis	lymphoblastoid	seeQTL
rs7504908	MEST	trans	lymphoblastoid	seeQTL
rs7504908	TUBB6	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12312600-12332600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr18:12314000-12333600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr18:12314200-12327800	Strong transcription	HUES6 Cell Line	embryonic stem cell
4	chr18:12314400-12342600	Weak transcription	Small Intestine	intestine
5	chr18:12316400-12333600	Weak transcription	Fetal Brain Male	brain
6	chr18:12318000-12331200	Strong transcription	HMEC	breast
7	chr18:12318400-12334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr18:12318600-12331600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr18:12319000-12333800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr18:12319000-12336800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr18:12320200-12331200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:12320400-12328000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr18:12320600-12331400	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr18:12320800-12348200	Strong transcription	Fetal Intestine Small	intestine
15	chr18:12321200-12331600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr18:12321200-12331600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr18:12321600-12330000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr18:12323000-12327800	Strong transcription	Placenta	Placenta
19	chr18:12323000-12330200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr18:12323000-12332400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr18:12323400-12342800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr18:12323600-12329800	Strong transcription	Fetal Thymus	thymus
23	chr18:12323800-12331400	Strong transcription	Primary T cells from cord blood	blood
24	chr18:12324200-12329800	Strong transcription	Fetal Lung	lung
25	chr18:12324400-12327800	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr18:12324400-12331400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr18:12324400-12331400	Strong transcription	Brain Germinal Matrix	brain
28	chr18:12324400-12331400	Strong transcription	Brain Hippocampus Middle	brain
29	chr18:12324400-12331800	Strong transcription	Thymus	Thymus
30	chr18:12324600-12327800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr18:12324600-12327800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr18:12324600-12331600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr18:12324800-12327800	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr18:12324800-12327800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr18:12324800-12327800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr18:12324800-12327800	Strong transcription	Brain Substantia Nigra	brain
37	chr18:12324800-12328000	Strong transcription	H9 Cell Line	embryonic stem cell
38	chr18:12324800-12328200	Strong transcription	A549	lung
39	chr18:12324800-12329800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr18:12324800-12329800	Strong transcription	Fetal Brain Female	brain
41	chr18:12324800-12330000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr18:12324800-12330000	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr18:12324800-12330000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr18:12324800-12330000	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr18:12324800-12330000	Strong transcription	Colonic Mucosa	Colon
46	chr18:12324800-12330000	Strong transcription	Ovary	ovary
47	chr18:12324800-12330000	Strong transcription	HepG2	liver
48	chr18:12324800-12330200	Strong transcription	NH-A	brain
49	chr18:12324800-12331200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr18:12324800-12331200	Strong transcription	GM12878-XiMat	blood

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