Variant report

Variant	rs7543769
Chromosome Location	chr1:175946722-175946723
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10158829	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs10494496	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10737316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798427	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs10798431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798433	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798435	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11803301	0.94[ASN][1000 genomes]
rs11806468	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs11809136	1.00[CEU][hapmap]
rs12038027	0.81[ASN][1000 genomes]
rs12239888	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1357337	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs1522637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs16849522	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1831447	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2039231	1.00[CHB][hapmap]
rs2039232	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2481627	1.00[CHB][hapmap]
rs2481639	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2481641	1.00[CHB][hapmap]
rs2481647	1.00[CHB][hapmap]
rs2481653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2481657	1.00[CHB][hapmap]
rs2481660	0.95[AMR][1000 genomes]
rs2502822	1.00[CHB][hapmap]
rs2502824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2502825	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2502826	1.00[CHB][hapmap]
rs2502832	1.00[CHB][hapmap]
rs2502834	1.00[CHB][hapmap]
rs2502835	1.00[CHB][hapmap]
rs2502836	1.00[CHB][hapmap]
rs2502841	1.00[CHB][hapmap]
rs2502842	1.00[CHB][hapmap]
rs2861629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3845368	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4304533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4543747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4652140	0.97[ASN][1000 genomes]
rs4652141	0.90[ASN][1000 genomes]
rs4652142	0.90[ASN][1000 genomes]
rs4652143	0.82[CHB][hapmap]
rs4652144	0.90[ASN][1000 genomes]
rs4652148	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs4652152	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs553852	1.00[CHB][hapmap]
rs559341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56952885	0.97[ASN][1000 genomes]
rs58325269	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58399286	0.90[ASN][1000 genomes]
rs598177	0.95[AMR][1000 genomes]
rs599326	1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60086820	0.90[ASN][1000 genomes]
rs602933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61132016	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425368	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs6425370	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672278	0.85[AMR][1000 genomes]
rs6688211	1.00[CHB][hapmap]
rs6704509	1.00[CHB][hapmap]
rs704825	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs704827	0.85[CHB][hapmap]
rs73035644	0.90[ASN][1000 genomes]
rs73035646	0.90[ASN][1000 genomes]
rs73038827	0.90[ASN][1000 genomes]
rs73038833	0.90[ASN][1000 genomes]
rs7517351	1.00[CHB][hapmap]
rs7521561	1.00[CHB][hapmap]
rs7522442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7524972	0.81[ASN][1000 genomes]
rs7536464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7539247	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7543882	0.90[ASN][1000 genomes]
rs7545043	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs7552181	1.00[CHB][hapmap]
rs7553184	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs796933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs796934	0.95[AMR][1000 genomes]
rs9783047	1.00[CHB][hapmap];0.81[ASN][1000 genomes]

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	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	nsv947452	chr1:175944970-175947820	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175897000-175953000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:175897600-175953200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:175897800-175952400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:175898600-175953200	Weak transcription	Pancreas	Pancrea
5	chr1:175899200-175953200	Weak transcription	Esophagus	oesophagus
6	chr1:175903400-175951400	Weak transcription	K562	blood
7	chr1:175904200-175956200	Weak transcription	Psoas Muscle	Psoas
8	chr1:175904600-175953000	Weak transcription	Right Ventricle	heart
9	chr1:175905000-175946800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:175906400-175952400	Weak transcription	Spleen	Spleen
11	chr1:175906400-175962600	Weak transcription	NH-A	brain
12	chr1:175906800-175952000	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:175907400-175950600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr1:175908000-175959400	Weak transcription	NHEK	skin
15	chr1:175909400-175948000	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:175911200-175947600	Weak transcription	Brain Hippocampus Middle	brain
17	chr1:175911200-175950400	Weak transcription	Fetal Heart	heart
18	chr1:175916400-175952200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr1:175917600-175953000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr1:175919000-175947800	Weak transcription	Brain Germinal Matrix	brain
21	chr1:175921400-175951200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr1:175922000-175952000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr1:175924600-175953200	Weak transcription	Gastric	stomach
24	chr1:175924600-175953200	Weak transcription	HepG2	liver
25	chr1:175924800-175947600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:175925000-175951800	Weak transcription	Brain Anterior Caudate	brain
27	chr1:175927000-175951200	Weak transcription	Fetal Brain Male	brain
28	chr1:175930200-175947600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:175930400-175947000	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:175930400-175951800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:175930400-175952200	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr1:175930600-175951400	Weak transcription	Fetal Kidney	kidney
33	chr1:175930800-175947600	Weak transcription	Fetal Stomach	stomach
34	chr1:175930800-175949600	Weak transcription	Ovary	ovary
35	chr1:175934200-175950400	Weak transcription	GM12878-XiMat	blood
36	chr1:175937400-175951400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr1:175938000-175951800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:175938200-175947600	Weak transcription	Brain Substantia Nigra	brain
39	chr1:175938200-175951800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr1:175938400-175950200	Weak transcription	HSMMtube	muscle
41	chr1:175938800-175950000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:175938800-175952200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr1:175939000-175951400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:175939400-175952200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:175940400-175953800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:175941000-175952600	Weak transcription	Colonic Mucosa	Colon
47	chr1:175941000-175953200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:175941200-175947400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:175941200-175947600	Weak transcription	Fetal Intestine Small	intestine
50	chr1:175941200-175947800	Weak transcription	Cortex derived primary cultured neurospheres	brain

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