Variant report

Variant	rs12065854
Chromosome Location	chr1:174906714-174906715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1002125	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10158096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs10489333	1.00[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10494493	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap]
rs10912849	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10912870	0.89[CHB][hapmap];0.93[CHD][hapmap]
rs12063802	0.86[EUR][1000 genomes]
rs12066247	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12068637	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12074821	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12087196	0.81[EUR][1000 genomes]
rs12087589	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12562194	0.80[EUR][1000 genomes]
rs12565944	0.80[EUR][1000 genomes]
rs12566477	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16847402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap]
rs16847450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs16847563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16847633	0.92[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16847706	0.83[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.93[TSI][hapmap]
rs2285209	0.81[EUR][1000 genomes]
rs28660133	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41266068	0.80[EUR][1000 genomes]
rs41266072	0.80[EUR][1000 genomes]
rs57366106	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61828068	0.82[EUR][1000 genomes]
rs61828081	0.82[EUR][1000 genomes]
rs61828087	0.85[EUR][1000 genomes]
rs61828088	0.85[EUR][1000 genomes]
rs61828117	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61828121	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61828143	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61828144	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61828148	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61828149	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61828151	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61828152	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61828156	0.80[EUR][1000 genomes]
rs61828157	0.80[EUR][1000 genomes]
rs7523516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1794782	chr1:174900761-174925112	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
4	chr1:174886000-174907200	Weak transcription	Primary T cells from cord blood	blood
5	chr1:174886400-174911600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:174889600-174907400	Weak transcription	Primary B cells from cord blood	blood
7	chr1:174891800-174908600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:174893400-174907600	Weak transcription	GM12878-XiMat	blood
9	chr1:174897400-174910000	Weak transcription	Gastric	stomach
10	chr1:174897800-174907200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:174898800-174910600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:174899800-174915200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:174900800-174907600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:174900800-174907600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:174900800-174911000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:174901000-174907800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:174901000-174909400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:174901000-174922200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:174901400-174907600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:174901600-174907200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:174901600-174907200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:174901600-174907400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:174901800-174908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:174902200-174909000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:174902600-174907600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:174902600-174908400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:174903800-174911000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:174904400-174907200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:174904600-174907600	Weak transcription	Fetal Stomach	stomach
30	chr1:174904800-174907600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:174905400-174907200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:174905600-174907200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:174905600-174907200	Weak transcription	Fetal Intestine Large	intestine
34	chr1:174905800-174907200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:174905800-174907800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:174905800-174910000	Weak transcription	Pancreas	Pancrea
37	chr1:174905800-174910600	Weak transcription	HepG2	liver
38	chr1:174905800-174911600	Weak transcription	Primary B cells from peripheral blood	blood

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