Variant report

Variant	rs9652931
Chromosome Location	chr18:12309529-12309530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:12309471-12310305	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr18:12307140-12311108	MCF10A-Er-Src	breast:	n/a	n/a
3	CHD2	chr18:12309509-12309944	GM12878	blood:	n/a	n/a
4	POLR2A	chr18:12304971-12316847	IMR90	lung:	n/a	n/a
5	CHD1	chr18:12306712-12310268	IMR90	lung:	n/a	chr18:12307601-12307611
6	POLR2A	chr18:12309511-12310034	GM12892	blood:	n/a	n/a
7	POLR2A	chr18:12309378-12310112	U87	brain:	n/a	n/a
8	POLR2A	chr18:12309372-12310215	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr18:12307184-12311267	U87	brain:	n/a	n/a
10	POLR2A	chr18:12307241-12311221	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr18:12309408-12310077	GM12878	blood:	n/a	n/a
12	POLR2A	chr18:12306708-12310326	U87	brain:	n/a	n/a
13	MXI1	chr18:12307097-12310263	IMR90	lung:	n/a	n/a
14	POLR2A	chr18:12307119-12310305	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr18:12307308-12310201	PFSK-1	brain:	n/a	n/a
16	POLR2A	chr18:12309394-12310070	U87	brain:	n/a	n/a
17	MYC	chr18:12309436-12310180	MCF10A-Er-Src	breast:	n/a	chr18:12309906-12309916
18	POLR2A	chr18:12309479-12310204	K562	blood:	n/a	n/a
19	POLR2A	chr18:12309449-12310034	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr18:12309412-12310039	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr18:12307430-12310239	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr18:12307036-12310287	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr18:12309423-12309952	K562	blood:	n/a	n/a
24	MTA3	chr18:12309511-12310110	GM12878	blood:	n/a	n/a
25	STAT3	chr18:12309456-12310293	MCF10A-Er-Src	breast:	n/a	chr18:12310102-12310113 chr18:12309993-12310000
26	HEY1	chr18:12309374-12310218	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12280564..12282806-chr18:12308373..12310089,2	MCF-7	breast:
2	chr18:12307735..12310451-chr18:12655693..12658579,2	MCF-7	breast:
3	chr18:12307737..12309568-chr20:45947449..45950208,2	MCF-7	breast:
4	chr18:12307869..12309956-chr18:12375801..12377728,3	MCF-7	breast:
5	chr18:12306891..12312604-chr18:12376208..12378768,5	K562	blood:
6	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:

No data

Variant related genes	Relation type
TUBB6	TF binding region
ENSG00000101040	Chromatin interaction
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000141385	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10853224	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11080567	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11267036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11548177	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11659246	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11660106	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11660222	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11663340	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11664255	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11664282	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12455756	0.86[EUR][1000 genomes]
rs12607250	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12607321	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12607378	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12954560	0.84[EUR][1000 genomes]
rs12959653	0.83[ASN][1000 genomes]
rs12959674	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12960267	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12963761	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12965912	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12970667	0.90[ASN][1000 genomes]
rs28625182	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34685983	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35242253	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796958	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796959	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796960	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4796962	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796963	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4797672	0.82[ASN][1000 genomes]
rs4797673	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4797674	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4797675	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58136410	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61604633	0.87[EUR][1000 genomes]
rs62097556	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6505749	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6505751	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7231304	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7233290	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7244254	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7244709	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7504558	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7504575	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7504616	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7505208	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7505255	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7505626	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083882	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8087843	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8098040	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8098700	0.82[ASN][1000 genomes]
rs8099636	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9303766	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9303767	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9303768	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9807444	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9945901	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9946172	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9946217	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9946347	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9949054	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9954945	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9958069	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9958525	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9964163	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9966470	0.87[EUR][1000 genomes]

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	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	nsv909401	chr18:12211483-12312075	Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv909402	chr18:12211483-12325222	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv909403	chr18:12231060-12325222	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	nsv1058661	chr18:12280366-12313865	Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	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
13	esv3316265	chr18:12307177-12309725	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
14	esv3316266	chr18:12307177-12309725	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9652931	TUBB6	cis	multi-tissue	Pritchard
rs9652931	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs9652931	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL
rs9652931	TUBB6	cis	Whole Blood	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12306600-12309600	Active TSS	Right Atrium	heart
2	chr18:12307000-12309600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr18:12307000-12309600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr18:12307000-12309600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr18:12307000-12309600	Active TSS	Colon Smooth Muscle	Colon
6	chr18:12307000-12309600	Active TSS	Rectal Smooth Muscle	rectum
7	chr18:12307000-12309800	Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr18:12307200-12309600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr18:12307200-12309600	Active TSS	Left Ventricle	heart
10	chr18:12307200-12309800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr18:12307200-12310000	Active TSS	Aorta	Aorta
12	chr18:12307400-12309600	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr18:12307400-12309600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
14	chr18:12307400-12309600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr18:12307400-12309600	Active TSS	Right Ventricle	heart
16	chr18:12307400-12310000	Active TSS	Esophagus	oesophagus
17	chr18:12307600-12309600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr18:12307600-12309600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:12307600-12309600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:12307600-12309600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr18:12307600-12309600	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr18:12307600-12309600	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr18:12307600-12309600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
24	chr18:12307600-12309600	Active TSS	Fetal Kidney	kidney
25	chr18:12307600-12309600	Active TSS	Rectal Mucosa Donor 31	rectum
26	chr18:12307600-12309600	Active TSS	A549	lung
27	chr18:12307600-12310200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
28	chr18:12307600-12310600	Active TSS	GM12878-XiMat	blood
29	chr18:12307800-12309600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr18:12307800-12309600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr18:12307800-12309600	Active TSS	NHEK	skin
32	chr18:12307800-12309800	Bivalent/Poised TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr18:12307800-12309800	Active TSS	Pancreas	Pancrea
34	chr18:12308000-12309600	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr18:12308200-12309600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr18:12308400-12309600	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr18:12308400-12310000	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr18:12308600-12309600	Active TSS	Fetal Heart	heart
39	chr18:12308600-12310000	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
40	chr18:12308800-12309600	Bivalent Enhancer	Fetal Brain Male	brain
41	chr18:12308800-12309600	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
42	chr18:12308800-12309600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
43	chr18:12308800-12309800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
44	chr18:12308800-12309800	Flanking Active TSS	Placenta	Placenta
45	chr18:12308800-12309800	Active TSS	Psoas Muscle	Psoas
46	chr18:12308800-12310000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
47	chr18:12308800-12311000	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
48	chr18:12308800-12311000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr18:12309000-12309600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr18:12309000-12309600	Flanking Active TSS	Fetal Muscle Leg	muscle

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