Variant report

Variant	rs12419172
Chromosome Location	chr11:85350822-85350823
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:85337741..85343545-chr11:85345780..85354384,11	MCF-7	breast:
2	chr11:85347047..85348575-chr11:85349849..85352834,2	MCF-7	breast:
3	chr11:85338250..85341391-chr11:85347882..85353212,5	MCF-7	breast:
4	chr11:85349221..85351425-chr11:85352555..85354593,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150672	Chromatin interaction
ENSG00000171204	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10501595	1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11234359	0.94[JPT][hapmap]
rs11820071	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1192	0.87[ASW][hapmap];0.89[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.81[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1214001	0.87[ASW][hapmap];0.89[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12417341	0.89[ASN][1000 genomes]
rs17148254	0.90[ASN][1000 genomes]
rs17148293	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17148306	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17208492	0.82[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17208519	1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17810659	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs188311	0.94[JPT][hapmap]
rs1892872	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1991923	0.88[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2162055	0.85[ASN][1000 genomes]
rs2290823	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2467059	0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs290175	0.94[JPT][hapmap]
rs290177	0.94[JPT][hapmap]
rs290178	0.81[ASN][1000 genomes]
rs290182	0.89[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs290186	0.91[CHD][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.84[ASN][1000 genomes]
rs290194	0.94[JPT][hapmap]
rs290196	0.94[JPT][hapmap]
rs290199	0.94[JPT][hapmap]
rs35844123	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4943925	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4944527	0.88[ASN][1000 genomes]
rs4944529	0.81[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4944531	1.00[CEU][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4944532	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs497698	0.84[ASN][1000 genomes]
rs510948	0.88[JPT][hapmap]
rs537266	0.94[JPT][hapmap]
rs537604	0.88[JPT][hapmap]
rs56579	0.97[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs573766	0.92[JPT][hapmap]
rs578324	0.94[JPT][hapmap]
rs58152312	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs583122	0.94[JPT][hapmap]
rs58931064	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs592712	0.88[JPT][hapmap]
rs60838923	0.83[ASN][1000 genomes]
rs609012	0.88[JPT][hapmap]
rs613973	1.00[JPT][hapmap]
rs639688	0.81[JPT][hapmap]
rs650036	0.94[JPT][hapmap]
rs653559	0.94[JPT][hapmap]
rs6592252	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6592253	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs681044	0.88[JPT][hapmap]
rs688741	0.94[JPT][hapmap]
rs7108132	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7115250	0.88[ASN][1000 genomes]
rs7119617	0.90[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7939217	0.84[ASN][1000 genomes]
rs7943586	0.88[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs881121	0.84[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs947861	0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs947862	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs947863	0.89[ASW][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv898047	chr11:85180409-85377707	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription 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	56 gene(s)	inside rSNPs	diseases
6	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12419172	CCDC89	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85340200-85351800	Weak transcription	Gastric	stomach
2	chr11:85340200-85352400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr11:85340400-85351000	Weak transcription	Esophagus	oesophagus
4	chr11:85340600-85352800	Weak transcription	Fetal Brain Male	brain
5	chr11:85340600-85358200	Weak transcription	Aorta	Aorta
6	chr11:85340800-85358200	Weak transcription	Fetal Stomach	stomach
7	chr11:85340800-85358200	Weak transcription	Right Ventricle	heart
8	chr11:85340800-85358200	Weak transcription	HSMMtube	muscle
9	chr11:85341000-85351600	Weak transcription	Thymus	Thymus
10	chr11:85341200-85354400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:85341200-85358000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:85341200-85358000	Weak transcription	NHLF	lung
13	chr11:85341200-85358200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:85341200-85358200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:85341200-85358200	Weak transcription	Spleen	Spleen
16	chr11:85341200-85358400	Weak transcription	Small Intestine	intestine
17	chr11:85341400-85354200	Weak transcription	Fetal Intestine Small	intestine
18	chr11:85341800-85353000	Weak transcription	Fetal Heart	heart
19	chr11:85342200-85358200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr11:85342400-85352600	Weak transcription	Psoas Muscle	Psoas
21	chr11:85342800-85352600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:85344600-85351000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:85345800-85358000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr11:85346000-85354400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr11:85346000-85358000	Weak transcription	HMEC	breast
26	chr11:85346000-85358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr11:85346000-85358200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:85346000-85358200	Weak transcription	Brain Angular Gyrus	brain
29	chr11:85346000-85358200	Weak transcription	Brain Substantia Nigra	brain
30	chr11:85346000-85358200	Weak transcription	Fetal Lung	lung
31	chr11:85346000-85358200	Weak transcription	NHEK	skin
32	chr11:85346400-85352600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr11:85346400-85354200	Weak transcription	Hela-S3	cervix
34	chr11:85346400-85358000	Weak transcription	HepG2	liver
35	chr11:85346400-85358200	Weak transcription	Lung	lung
36	chr11:85346600-85358200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:85346800-85358000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr11:85346800-85358200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr11:85347200-85357800	Weak transcription	GM12878-XiMat	blood
40	chr11:85347200-85358200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr11:85347400-85351200	Weak transcription	NH-A	brain
42	chr11:85347400-85358000	Weak transcription	Colon Smooth Muscle	Colon
43	chr11:85347400-85358000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr11:85347600-85351200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr11:85347600-85351200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr11:85347600-85354200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr11:85347600-85358000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr11:85347600-85358200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr11:85347600-85358200	Weak transcription	Brain Anterior Caudate	brain
50	chr11:85347800-85351600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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