Variant report

Variant	rs12138008
Chromosome Location	chr1:176007224-176007225
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:176007125..176010101-chr1:176013054..176015518,2	K562	blood:
2	chr1:176004510..176007370-chr1:176012270..176013775,2	K562	blood:
3	chr1:175998716..176001033-chr1:176006174..176008100,2	K562	blood:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10494495	0.80[JPT][hapmap]
rs10753117	0.85[JPT][hapmap]
rs10798434	0.81[JPT][hapmap]
rs10798442	0.86[JPT][hapmap]
rs10798445	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs10798446	0.82[JPT][hapmap]
rs10913118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10913135	0.80[JPT][hapmap]
rs10913137	0.82[JPT][hapmap]
rs10913143	0.81[JPT][hapmap]
rs10913144	0.81[JPT][hapmap]
rs10913147	0.82[JPT][hapmap]
rs11810706	0.95[CEU][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs12029090	0.84[JPT][hapmap]
rs12033847	0.85[JPT][hapmap]
rs12049077	0.82[JPT][hapmap]
rs12135395	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12404596	0.85[JPT][hapmap]
rs12723724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12729524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12741940	0.87[AMR][1000 genomes]
rs12756741	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16849486	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17354120	0.80[JPT][hapmap]
rs1974142	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2039230	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap]
rs2175177	0.83[JPT][hapmap]
rs2457418	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2481628	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2481630	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2481631	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs2481633	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2481646	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2481655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2481658	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2481662	0.81[EUR][1000 genomes]
rs2487144	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs2502823	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2502829	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2502831	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs2502845	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs34973462	0.91[EUR][1000 genomes]
rs3934392	0.87[AMR][1000 genomes]
rs3962371	0.81[CEU][hapmap]
rs4409605	0.80[JPT][hapmap]
rs520661	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs617078	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs6660080	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6665385	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs6678628	0.81[JPT][hapmap]
rs6678812	0.80[JPT][hapmap]
rs668154	0.85[AFR][1000 genomes]
rs6682194	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6697860	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs679728	0.84[CEU][hapmap]
rs704829	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs704834	0.84[CEU][hapmap]
rs7517503	0.80[JPT][hapmap]
rs7530719	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7549160	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs791743	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs791751	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs791752	0.85[AFR][1000 genomes]
rs791753	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs813180	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs9425447	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs944365	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1823794	chr1:175869554-176311778	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv872561	chr1:175949646-176092167	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872562	chr1:175949646-176141866	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872563	chr1:175949646-176184625	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv1835152	chr1:175996260-176012807	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175957800-176022000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr1:175974600-176014200	Weak transcription	Colon Smooth Muscle	Colon
3	chr1:175975800-176016200	Weak transcription	HSMMtube	muscle
4	chr1:175976400-176014400	Weak transcription	Brain Angular Gyrus	brain
5	chr1:175976600-176009400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:175976800-176046000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:175978200-176007400	Weak transcription	Brain Germinal Matrix	brain
8	chr1:175978200-176050600	Weak transcription	Aorta	Aorta
9	chr1:175978400-176014000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:175978400-176014800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:175978400-176017800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:175978400-176069000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:175979200-176011800	Weak transcription	Brain Anterior Caudate	brain
14	chr1:175979400-176009200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:175979400-176012200	Weak transcription	HepG2	liver
16	chr1:175979600-176010600	Weak transcription	Right Ventricle	heart
17	chr1:175979600-176012000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr1:175979600-176045400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:175979800-176014400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:175980200-176028000	Weak transcription	K562	blood
21	chr1:175981400-176009200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:175982000-176009800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr1:175982200-176009400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:175982200-176009400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr1:175982200-176012200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:175983400-176010600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr1:175988400-176009400	Weak transcription	Lung	lung
28	chr1:175989000-176009400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:175989000-176009600	Weak transcription	Esophagus	oesophagus
30	chr1:175989400-176009400	Weak transcription	Fetal Muscle Leg	muscle
31	chr1:175989800-176009400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:175989800-176009400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:175989800-176010600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr1:175989800-176010600	Weak transcription	Spleen	Spleen
35	chr1:175989800-176036400	Weak transcription	Pancreas	Pancrea
36	chr1:175990200-176009400	Weak transcription	Gastric	stomach
37	chr1:175990400-176008800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr1:175994200-176065200	Weak transcription	Psoas Muscle	Psoas
39	chr1:175996800-176009400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr1:175997000-176007800	Weak transcription	Placenta	Placenta
41	chr1:175997600-176007600	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:175998200-176009400	Weak transcription	Left Ventricle	heart
43	chr1:175998200-176009400	Weak transcription	Ovary	ovary
44	chr1:175999000-176017000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr1:175999200-176008600	Strong transcription	Primary B cells from peripheral blood	blood
46	chr1:176000600-176014800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr1:176001800-176016200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:176002000-176008000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:176002000-176009600	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr1:176002000-176010600	Weak transcription	Thymus	Thymus

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