Variant report

Variant	rs12121834
Chromosome Location	chr1:180067914-180067915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180067842..180070098-chr1:180124230..180125960,2	MCF-7	breast:
2	chr1:180067800..180070199-chr1:180137539..180139968,2	MCF-7	breast:
3	chr1:180067070..180070022-chr1:180093157..180094949,2	K562	blood:
4	chr1:180064498..180066210-chr1:180067083..180069817,2	K562	blood:

Extended variants
information (count: 113 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10442618	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10494524	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs12116940	0.84[EUR][1000 genomes]
rs12118985	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119130	0.84[EUR][1000 genomes]
rs12120418	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12121845	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123139	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123201	0.92[ASN][1000 genomes]
rs12123560	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs12124265	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125556	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125592	0.84[EUR][1000 genomes]
rs12125693	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12125893	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126967	0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12127784	0.84[EUR][1000 genomes]
rs12129115	0.82[EUR][1000 genomes]
rs12130397	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12130479	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12130489	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12130675	0.92[ASN][1000 genomes]
rs12131200	0.81[TSI][hapmap]
rs12132694	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs12134536	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135751	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs12135828	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138201	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12138429	0.84[EUR][1000 genomes]
rs12138974	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139323	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs12139412	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs12139761	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140235	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140589	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12140868	1.00[CEU][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141817	1.00[CEU][hapmap];0.92[ASN][1000 genomes]
rs12144275	0.92[ASN][1000 genomes]
rs12144328	0.84[EUR][1000 genomes]
rs12144346	0.81[TSI][hapmap]
rs12144352	0.81[TSI][hapmap]
rs12145411	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs12184265	0.82[EUR][1000 genomes]
rs12184270	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843139	1.00[CEU][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855014	0.89[CHD][hapmap];0.84[ASN][1000 genomes]
rs16855019	1.00[CEU][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs16855021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs16855022	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.92[ASN][1000 genomes]
rs16855025	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.92[ASN][1000 genomes]
rs16855048	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.80[YRI][hapmap];0.92[ASN][1000 genomes]
rs16855049	0.92[CEU][hapmap];0.92[ASN][1000 genomes]
rs16855052	0.92[ASN][1000 genomes]
rs16855070	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16855099	0.92[ASN][1000 genomes]
rs16855103	0.92[ASN][1000 genomes]
rs16855107	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855110	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855125	1.00[CEU][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855130	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855144	0.92[ASN][1000 genomes]
rs16855259	0.92[ASN][1000 genomes]
rs16855268	1.00[CEU][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855270	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16855286	0.92[ASN][1000 genomes]
rs16855289	0.89[CHD][hapmap];0.88[ASN][1000 genomes]
rs17371159	0.81[TSI][hapmap]
rs17371308	0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs1801795	0.84[EUR][1000 genomes]
rs3856048	0.92[ASN][1000 genomes]
rs41267622	0.92[ASN][1000 genomes]
rs4266842	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4278337	1.00[CEU][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4460595	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57165548	0.92[ASN][1000 genomes]
rs58316647	0.84[ASN][1000 genomes]
rs58463801	0.92[ASN][1000 genomes]
rs58749862	0.84[ASN][1000 genomes]
rs59132689	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60064848	0.92[ASN][1000 genomes]
rs60895715	0.92[ASN][1000 genomes]
rs60927554	0.92[ASN][1000 genomes]
rs60972670	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60976015	0.92[ASN][1000 genomes]
rs61014689	0.92[ASN][1000 genomes]
rs61242295	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032352	0.92[ASN][1000 genomes]
rs73032390	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032397	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034408	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034486	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73039990	0.92[ASN][1000 genomes]
rs73039999	0.92[ASN][1000 genomes]
rs73040001	0.92[ASN][1000 genomes]
rs9699897	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv466228	chr1:179944901-180067988	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv548340	chr1:179944901-180067988	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv520322	chr1:179944901-180071987	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv548341	chr1:179945390-180067914	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv520278	chr1:179945390-180093066	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv548342	chr1:179958809-180067988	Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv548343	chr1:179958809-180071987	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv548344	chr1:179960787-180071987	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
13	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
14	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
15	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
16	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
17	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
18	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	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
rs12121834	CEP350	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179970800-180076800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr1:179983600-180083400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:180000800-180083400	Strong transcription	Primary T helper cells fromperipheralblood	blood
4	chr1:180002400-180085000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:180009000-180069600	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr1:180009200-180070000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:180013000-180080000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:180029600-180084800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:180030000-180073000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:180040800-180082200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr1:180042000-180082600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:180043000-180068400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:180044800-180077200	Weak transcription	Small Intestine	intestine
14	chr1:180048800-180082200	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr1:180049000-180076800	Strong transcription	Primary B cells from cord blood	blood
16	chr1:180052800-180082600	Strong transcription	Fetal Thymus	thymus
17	chr1:180052800-180085800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:180053000-180072400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:180053000-180083000	Strong transcription	Liver	Liver
20	chr1:180053200-180072600	Strong transcription	Fetal Intestine Large	intestine
21	chr1:180053600-180068000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr1:180054000-180068200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:180054000-180082600	Strong transcription	Dnd41	blood
24	chr1:180054400-180072800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr1:180054600-180079400	Weak transcription	Fetal Brain Male	brain
26	chr1:180056800-180068600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:180057000-180068600	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:180057200-180068400	Strong transcription	Primary T cells from cord blood	blood
29	chr1:180057400-180068400	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr1:180057600-180082600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr1:180057600-180082800	Strong transcription	Adipose Nuclei	Adipose
32	chr1:180058000-180069400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr1:180058000-180070000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:180059000-180072600	Strong transcription	Duodenum Mucosa	Duodenum
35	chr1:180059200-180069000	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr1:180059200-180073000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr1:180059200-180076000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:180059600-180069600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:180059600-180073600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:180060000-180072800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:180060200-180068200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:180060200-180068400	Strong transcription	Brain Hippocampus Middle	brain
43	chr1:180060200-180072600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:180060800-180068800	Strong transcription	Primary hematopoietic stem cells	blood
45	chr1:180061000-180069800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:180061000-180070600	Weak transcription	Gastric	stomach
47	chr1:180061000-180071200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:180061200-180070600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:180061200-180070600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:180062200-180068400	Strong transcription	Fetal Muscle Leg	muscle

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