Variant report

Variant	rs12959653
Chromosome Location	chr18:12319332-12319333
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12307701..12309556-chr18:12318033..12320333,2	MCF-7	breast:
2	chr18:12314718..12316878-chr18:12317452..12319661,2	MCF-7	breast:
3	chr18:12312656..12314988-chr18:12316506..12319573,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10853224	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11080567	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11267036	0.82[ASN][1000 genomes]
rs11548177	0.83[ASN][1000 genomes]
rs11660222	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12607321	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12607378	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12959674	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12960267	0.83[ASN][1000 genomes]
rs12963761	0.82[ASN][1000 genomes]
rs35242253	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796958	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796959	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4796960	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4796962	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs4796963	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4797672	0.81[ASN][1000 genomes]
rs4797673	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797674	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797675	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58136410	0.83[ASN][1000 genomes]
rs6505749	0.83[ASN][1000 genomes]
rs6505751	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7244254	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7504558	0.82[ASN][1000 genomes]
rs7504575	0.82[ASN][1000 genomes]
rs7505208	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7505255	0.83[ASN][1000 genomes]
rs7505626	0.83[ASN][1000 genomes]
rs8083882	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8087843	0.83[ASN][1000 genomes]
rs8098040	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8098700	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8099636	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9652931	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12959653	MC1R///TUBB3	trans	lymphoblastoid	RTeQTL
rs12959653	TUBB6	cis	Whole Blood	GTEx
rs12959653	TUBB6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12310000-12324800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:12310000-12325800	Weak transcription	Fetal Kidney	kidney
3	chr18:12310200-12320400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr18:12310200-12324800	Weak transcription	HepG2	liver
5	chr18:12310600-12322800	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr18:12311000-12323200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:12311000-12324800	Weak transcription	Spleen	Spleen
8	chr18:12312600-12320400	Weak transcription	Brain Angular Gyrus	brain
9	chr18:12312600-12325000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr18:12312600-12332600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:12312800-12324800	Weak transcription	Colonic Mucosa	Colon
12	chr18:12312800-12324800	Weak transcription	Fetal Brain Female	brain
13	chr18:12313000-12320800	Weak transcription	Fetal Intestine Small	intestine
14	chr18:12313200-12320400	Weak transcription	Liver	Liver
15	chr18:12313400-12319600	Genic enhancers	Fetal Muscle Leg	muscle
16	chr18:12314000-12333600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr18:12314200-12323000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr18:12314200-12327800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr18:12314400-12342600	Weak transcription	Small Intestine	intestine
20	chr18:12314600-12324400	Weak transcription	Brain Germinal Matrix	brain
21	chr18:12314800-12320600	Weak transcription	Fetal Intestine Large	intestine
22	chr18:12315600-12324800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr18:12316200-12319800	Enhancers	Primary B cells from peripheral blood	blood
24	chr18:12316200-12320600	Weak transcription	Brain Substantia Nigra	brain
25	chr18:12316200-12324600	Weak transcription	Gastric	stomach
26	chr18:12316200-12325000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr18:12316400-12320600	Weak transcription	Brain Anterior Caudate	brain
28	chr18:12316400-12323000	Weak transcription	Fetal Lung	lung
29	chr18:12316400-12333600	Weak transcription	Fetal Brain Male	brain
30	chr18:12316600-12324400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr18:12316600-12324800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr18:12316600-12327000	Weak transcription	Stomach Mucosa	stomach
33	chr18:12316800-12320400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr18:12316800-12320600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr18:12316800-12321600	Strong transcription	NHEK	skin
36	chr18:12316800-12327600	Strong transcription	HUVEC	blood vessel
37	chr18:12317600-12324800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr18:12317800-12322200	Strong transcription	NH-A	brain
39	chr18:12318000-12321000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr18:12318000-12321200	Strong transcription	HSMM	muscle
41	chr18:12318000-12325000	Weak transcription	Hela-S3	cervix
42	chr18:12318000-12331200	Strong transcription	HMEC	breast
43	chr18:12318200-12320400	Strong transcription	Osteobl	bone
44	chr18:12318400-12320400	Strong transcription	HSMMtube	muscle
45	chr18:12318400-12320600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr18:12318400-12320800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr18:12318400-12321200	Strong transcription	Muscle Satellite Cultured Cells	--
48	chr18:12318400-12321400	Weak transcription	Pancreas	Pancrea
49	chr18:12318400-12324800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr18:12318400-12334800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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