Variant report

Variant	rs1941222
Chromosome Location	chr18:12374362-12374363
allele	A/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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:12305136..12307294-chr18:12373188..12375992,2	K562	blood:
2	chr18:12354405..12356233-chr18:12373233..12375178,2	K562	blood:
3	chr18:12373675..12375792-chr18:12443379..12445132,2	K562	blood:
4	chr18:12354655..12356676-chr18:12372302..12374649,2	K562	blood:
5	chr18:12373949..12376848-chr18:12946851..12949234,5	K562	blood:
6	chr18:12372255..12374717-chr18:12702153..12705410,3	K562	blood:
7	chr18:12369983..12374854-chr18:12375235..12379102,8	MCF-7	breast:
8	chr18:12374049..12378632-chr18:12655494..12660049,8	K562	blood:
9	chr18:12352685..12355355-chr18:12373125..12375280,2	MCF-7	breast:
10	chr18:12372972..12377735-chr18:12656683..12660675,6	K562	blood:
11	chr18:12305251..12310573-chr18:12373540..12378768,12	K562	blood:
12	chr18:12373949..12378992-chr18:12946352..12949410,8	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134278	Chromatin interaction
ENSG00000215527	Chromatin interaction
ENSG00000141385	Chromatin interaction
ENSG00000101624	Chromatin interaction
ENSG00000085415	Chromatin interaction
ENSG00000128789	Chromatin interaction
ENSG00000176014	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10853225	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11080564	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs11080571	0.85[CEU][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs11080572	0.85[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1129115	0.86[CEU][hapmap];0.81[JPT][hapmap]
rs11553521	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11662523	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11664216	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11875938	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12455273	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12456857	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs12604732	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12954686	0.80[EUR][1000 genomes]
rs12968089	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12968566	0.84[EUR][1000 genomes]
rs1547858	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003881	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298543	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2509510	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28372882	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35968035	0.87[ASN][1000 genomes]
rs3786260	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs478088	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4797677	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4797680	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs553091	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs566960	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs693449	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7231182	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7231409	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7235237	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7235296	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7407640	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7504908	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7504974	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap]
rs7505834	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs8092506	0.80[CEU][hapmap];0.85[JPT][hapmap]
rs8093375	0.95[CEU][hapmap]
rs8097342	0.85[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9303769	0.85[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9303770	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9303771	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9635829	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9956171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9960103	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9964406	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[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	nsv1060728	chr18:12364077-12410409	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1941222	TUBB6	cis	Whole Blood	GTEx
rs1941222	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	chr18:12359200-12376000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:12359800-12375800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr18:12367600-12376000	Weak transcription	Fetal Kidney	kidney
4	chr18:12367800-12374400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr18:12367800-12375400	Weak transcription	HMEC	breast
6	chr18:12368800-12374400	Weak transcription	Fetal Brain Male	brain
7	chr18:12368800-12375400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr18:12369400-12374600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr18:12369400-12374600	Weak transcription	Adipose Nuclei	Adipose
10	chr18:12369400-12374600	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr18:12369400-12375000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr18:12369400-12375000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr18:12369400-12375400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr18:12369400-12375600	Weak transcription	A549	lung
15	chr18:12369400-12375800	Weak transcription	NHLF	lung
16	chr18:12369400-12376000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr18:12369600-12374600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr18:12369600-12374600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr18:12369600-12375000	Weak transcription	Placenta	Placenta
20	chr18:12369600-12375000	Weak transcription	Spleen	Spleen
21	chr18:12369600-12375200	Weak transcription	Primary B cells from cord blood	blood
22	chr18:12369600-12375400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr18:12369600-12375400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr18:12369600-12375400	Weak transcription	Esophagus	oesophagus
25	chr18:12370000-12375200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr18:12370400-12375800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr18:12370800-12374800	Weak transcription	Fetal Muscle Trunk	muscle
28	chr18:12370800-12375400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr18:12370800-12376000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr18:12371000-12375800	Enhancers	Thymus	Thymus
31	chr18:12371000-12376000	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr18:12371000-12376000	Enhancers	Fetal Thymus	thymus
33	chr18:12371200-12376000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr18:12371400-12374600	Enhancers	Primary T cells from cord blood	blood
35	chr18:12371400-12375800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr18:12371400-12376000	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr18:12371400-12376000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr18:12371400-12376000	Enhancers	Stomach Mucosa	stomach
39	chr18:12371400-12376200	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr18:12371600-12375200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr18:12371800-12375000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr18:12371800-12375800	Enhancers	Small Intestine	intestine
43	chr18:12372000-12375200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr18:12372000-12375400	Enhancers	Pancreas	Pancrea
45	chr18:12372400-12374400	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr18:12372400-12374600	Enhancers	Psoas Muscle	Psoas
47	chr18:12372400-12374800	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr18:12372400-12375000	Enhancers	Brain Substantia Nigra	brain
49	chr18:12372400-12375000	Genic enhancers	NHEK	skin
50	chr18:12372400-12375800	Enhancers	Liver	Liver

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