Variant report

Variant	rs12744504
Chromosome Location	chr1:173415547-173415548
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr1:173414901-173415561	U2OS	brain:	n/a	n/a
2	STAT3	chr1:173415351-173415551	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173414044..173416601-chr1:173422234..173425092,2	K562	blood:

Variant related genes	Relation type
ENSG00000203739	TF binding region

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

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10737301	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753078	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10753079	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10753080	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10798290	0.81[CHB][hapmap]
rs10912624	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10912626	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10912641	0.95[CHB][hapmap];0.80[JPT][hapmap]
rs10912643	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12026427	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12026677	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs12037210	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12039524	0.82[CEU][hapmap]
rs12058528	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12065426	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12077271	0.82[EUR][1000 genomes]
rs12080769	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12565753	0.83[EUR][1000 genomes]
rs12724371	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12745058	0.83[EUR][1000 genomes]
rs12753631	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12760501	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1461014	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1886639	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs33942654	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33951697	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34025182	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34259759	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34296122	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34331061	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34332254	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34919111	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35065145	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35379498	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35607505	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35632090	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35831548	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35845062	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36058163	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3934575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3934576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244196	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4294450	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4310474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4462186	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4539167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57032935	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61826747	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826748	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61826749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61826753	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61828886	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61828887	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61828888	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6425232	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425251	0.80[CHB][hapmap]
rs6660804	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66683313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670071	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6671141	0.94[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6687872	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6696443	0.86[EUR][1000 genomes]
rs6699094	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68193118	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72637251	0.81[ASN][1000 genomes]
rs7314	0.84[CEU][hapmap]
rs7413754	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7516544	0.83[EUR][1000 genomes]
rs7520641	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7521536	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7524403	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7524592	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7525100	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7529089	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7529377	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7530469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540065	0.84[CEU][hapmap]
rs7541082	0.81[CHB][hapmap]
rs7549074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912767	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831915	chr1:173268424-173482157	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173376200-173429000	Weak transcription	Gastric	stomach
2	chr1:173387600-173429000	Weak transcription	Lung	lung
3	chr1:173391800-173429000	Weak transcription	Ovary	ovary
4	chr1:173399400-173424200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:173399800-173415600	Weak transcription	Liver	Liver
6	chr1:173400200-173421000	Weak transcription	Psoas Muscle	Psoas
7	chr1:173400200-173422800	Weak transcription	NH-A	brain
8	chr1:173400400-173429000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:173400600-173428800	Weak transcription	Fetal Stomach	stomach
10	chr1:173400800-173420600	Weak transcription	Hela-S3	cervix
11	chr1:173400800-173421000	Weak transcription	Colon Smooth Muscle	Colon
12	chr1:173400800-173422800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr1:173400800-173429000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr1:173400800-173429000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:173401000-173415600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:173401000-173418000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:173401000-173421000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:173401000-173421000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:173401000-173422800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr1:173401000-173428800	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:173401000-173429000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr1:173401000-173429000	Weak transcription	Left Ventricle	heart
23	chr1:173401200-173422800	Weak transcription	HSMM	muscle
24	chr1:173401800-173429000	Weak transcription	Primary B cells from cord blood	blood
25	chr1:173404200-173429000	Weak transcription	Adipose Nuclei	Adipose
26	chr1:173404200-173429000	Weak transcription	Right Ventricle	heart
27	chr1:173404400-173423000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:173408800-173422800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:173408800-173422800	Weak transcription	HSMMtube	muscle
30	chr1:173408800-173422800	Weak transcription	K562	blood
31	chr1:173408800-173429000	Weak transcription	Brain Substantia Nigra	brain
32	chr1:173408800-173429000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:173409000-173415600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:173409000-173428800	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr1:173409000-173428800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:173409000-173429200	Weak transcription	Aorta	Aorta
37	chr1:173411400-173415800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:173411400-173427000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr1:173411600-173428800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr1:173413400-173429200	Weak transcription	Placenta	Placenta
41	chr1:173414600-173416200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
42	chr1:173414600-173416800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
43	chr1:173414600-173429000	Weak transcription	Thymus	Thymus
44	chr1:173414800-173416600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:173414800-173416800	ZNF genes & repeats	GM12878-XiMat	blood
46	chr1:173415000-173415600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr1:173415000-173416200	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:173415000-173416400	ZNF genes & repeats	Fetal Lung	lung
49	chr1:173415000-173417400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
50	chr1:173415000-173417600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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