Variant report

Variant	rs9966470
Chromosome Location	chr18:12353178-12353179
allele	A/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	chr18:12353108-12353233	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12352685..12355355-chr18:12373125..12375280,2	MCF-7	breast:

Variant related genes	Relation type
AFG3L2	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10853224	0.93[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs11080567	0.93[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs11267036	0.87[EUR][1000 genomes]
rs11548177	0.85[EUR][1000 genomes]
rs11659246	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11660106	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11660222	0.93[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs11661684	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11661708	0.88[ASN][1000 genomes]
rs11663340	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11664255	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11664282	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11872615	0.87[ASN][1000 genomes]
rs12327346	0.85[ASN][1000 genomes]
rs12607250	0.83[EUR][1000 genomes]
rs12607321	0.93[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap]
rs12607378	0.82[EUR][1000 genomes]
rs12960267	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs12960302	0.93[CEU][hapmap];0.93[JPT][hapmap]
rs12963761	0.85[EUR][1000 genomes]
rs12965912	0.83[EUR][1000 genomes]
rs12970667	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs28470464	0.87[ASN][1000 genomes]
rs28823942	0.85[ASN][1000 genomes]
rs35242253	0.82[EUR][1000 genomes]
rs3819091	0.93[CHB][hapmap];0.93[ASN][1000 genomes]
rs4796958	0.81[EUR][1000 genomes]
rs4796960	0.93[CEU][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs4796962	0.82[EUR][1000 genomes]
rs4796963	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs4797673	0.93[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs4797674	0.82[EUR][1000 genomes]
rs4797675	0.82[EUR][1000 genomes]
rs58136410	0.87[EUR][1000 genomes]
rs6416994	0.88[ASN][1000 genomes]
rs6505749	0.87[EUR][1000 genomes]
rs6505751	0.82[EUR][1000 genomes]
rs7231304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7233290	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7235929	0.88[ASN][1000 genomes]
rs7237135	0.91[ASN][1000 genomes]
rs7244254	0.82[EUR][1000 genomes]
rs72875309	0.93[ASN][1000 genomes]
rs7504558	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes]
rs7504575	0.85[EUR][1000 genomes]
rs7504616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7505208	0.82[EUR][1000 genomes]
rs7505255	0.87[EUR][1000 genomes]
rs7505626	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes]
rs8083882	0.93[CEU][hapmap];0.80[CHB][hapmap];0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs8087843	0.87[EUR][1000 genomes]
rs8098040	0.93[JPT][hapmap];0.82[EUR][1000 genomes]
rs8099636	0.82[EUR][1000 genomes]
rs9303766	0.93[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs9303767	0.83[EUR][1000 genomes]
rs9303768	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs9652931	0.87[EUR][1000 genomes]
rs9807444	0.93[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.83[EUR][1000 genomes]
rs9944742	0.88[ASN][1000 genomes]
rs9945901	0.82[EUR][1000 genomes]
rs9946108	0.88[ASN][1000 genomes]
rs9946172	0.84[EUR][1000 genomes]
rs9946217	0.83[EUR][1000 genomes]
rs9946347	0.83[EUR][1000 genomes]
rs9949054	0.83[EUR][1000 genomes]
rs9950665	0.89[ASN][1000 genomes]
rs9958069	0.83[EUR][1000 genomes]
rs9958525	0.83[EUR][1000 genomes]
rs9964041	0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9964437	0.88[ASN][1000 genomes]
rs9964720	0.88[ASN][1000 genomes]

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	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
5	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
6	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
7	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
8	nsv819744	chr18:12351281-12354053	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9966470	MGC4083	cis	multi-tissue	Pritchard
rs9966470	TUBB6	cis	multi-tissue	Pritchard
rs9966470	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL
rs9966470	TUBB6	Cis_1M	lymphoblastoid	RTeQTL
rs9966470	TUBB6	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12326200-12366400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr18:12333200-12362200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr18:12333200-12370800	Strong transcription	Fetal Muscle Trunk	muscle
4	chr18:12333200-12371200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr18:12333400-12366600	Strong transcription	Sigmoid Colon	Sigmoid Colon
6	chr18:12333400-12370200	Strong transcription	Fetal Thymus	thymus
7	chr18:12333400-12370800	Strong transcription	Fetal Muscle Leg	muscle
8	chr18:12333400-12371400	Strong transcription	Fetal Stomach	stomach
9	chr18:12333600-12356800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr18:12333600-12358200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr18:12333600-12361800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr18:12333600-12362600	Strong transcription	Adipose Nuclei	Adipose
13	chr18:12333600-12364000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr18:12333600-12366400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr18:12333600-12369600	Strong transcription	Placenta	Placenta
16	chr18:12333600-12369800	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr18:12333800-12353200	Strong transcription	Fetal Brain Female	brain
18	chr18:12333800-12357000	Strong transcription	Brain Anterior Caudate	brain
19	chr18:12333800-12360200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr18:12333800-12369400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr18:12334000-12369400	Strong transcription	Primary B cells from peripheral blood	blood
22	chr18:12335600-12362600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr18:12337000-12367600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr18:12337000-12374200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr18:12337200-12359800	Strong transcription	Fetal Intestine Large	intestine
26	chr18:12337200-12369400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr18:12337400-12354200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:12337400-12369800	Strong transcription	Liver	Liver
29	chr18:12337400-12370400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr18:12337800-12357000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr18:12337800-12360200	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:12337800-12360600	Strong transcription	Duodenum Mucosa	Duodenum
33	chr18:12337800-12369600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr18:12337800-12370800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr18:12338600-12359600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr18:12339200-12368800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr18:12339800-12354000	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr18:12339800-12359600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr18:12339800-12362000	Strong transcription	Stomach Smooth Muscle	stomach
40	chr18:12339800-12370200	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr18:12339800-12371400	Strong transcription	Dnd41	blood
42	chr18:12340000-12353400	Strong transcription	HSMM	muscle
43	chr18:12340000-12357000	Strong transcription	Colon Smooth Muscle	Colon
44	chr18:12340000-12361800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr18:12340000-12362000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr18:12340000-12365000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr18:12340000-12369400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr18:12340000-12369400	Strong transcription	HepG2	liver
49	chr18:12340000-12369600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr18:12340000-12370800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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