Variant report

Variant	rs12072553
Chromosome Location	chr1:173983663-173983664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173975275..173977152-chr1:173983041..173985333,2	K562	blood:
2	chr1:173982774..173988202-chr1:173988612..173994506,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224977	Chromatin interaction
ENSG00000135870	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10489892	1.00[EUR][1000 genomes]
rs10489893	1.00[EUR][1000 genomes]
rs10912687	1.00[EUR][1000 genomes]
rs10912688	1.00[EUR][1000 genomes]
rs10912693	1.00[EUR][1000 genomes]
rs10912699	1.00[EUR][1000 genomes]
rs10912700	1.00[EUR][1000 genomes]
rs10912701	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912707	1.00[EUR][1000 genomes]
rs10912708	1.00[EUR][1000 genomes]
rs10912711	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10912712	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10912725	1.00[EUR][1000 genomes]
rs10912742	1.00[EUR][1000 genomes]
rs10912743	1.00[EUR][1000 genomes]
rs10912744	1.00[EUR][1000 genomes]
rs10912748	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1135333	1.00[EUR][1000 genomes]
rs12057220	1.00[EUR][1000 genomes]
rs12057440	1.00[EUR][1000 genomes]
rs12058498	1.00[EUR][1000 genomes]
rs12059636	1.00[EUR][1000 genomes]
rs12060967	1.00[EUR][1000 genomes]
rs12061013	1.00[EUR][1000 genomes]
rs12062801	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12063273	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12063296	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12064818	1.00[EUR][1000 genomes]
rs12065194	1.00[EUR][1000 genomes]
rs12067109	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12067191	1.00[EUR][1000 genomes]
rs12068440	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12069446	1.00[EUR][1000 genomes]
rs12070328	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12073448	1.00[EUR][1000 genomes]
rs12077462	1.00[EUR][1000 genomes]
rs12078222	1.00[EUR][1000 genomes]
rs12078471	1.00[EUR][1000 genomes]
rs12078645	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12078817	1.00[EUR][1000 genomes]
rs12079240	1.00[EUR][1000 genomes]
rs12079274	1.00[EUR][1000 genomes]
rs12079650	1.00[EUR][1000 genomes]
rs12081595	1.00[EUR][1000 genomes]
rs12084213	1.00[EUR][1000 genomes]
rs12084911	1.00[EUR][1000 genomes]
rs12086246	0.93[AFR][1000 genomes]
rs12090507	1.00[EUR][1000 genomes]
rs12092291	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12096013	1.00[EUR][1000 genomes]
rs1322773	1.00[EUR][1000 genomes]
rs1322781	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1956522	1.00[EUR][1000 genomes]
rs2227611	1.00[EUR][1000 genomes]
rs2227622	1.00[EUR][1000 genomes]
rs57586767	1.00[EUR][1000 genomes]
rs59090917	1.00[EUR][1000 genomes]
rs6673147	1.00[EUR][1000 genomes]
rs6682041	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6684147	1.00[EUR][1000 genomes]
rs74126415	1.00[EUR][1000 genomes]
rs7550107	1.00[EUR][1000 genomes]
rs874342	1.00[EUR][1000 genomes]
rs9425413	1.00[EUR][1000 genomes]
rs9425414	1.00[EUR][1000 genomes]
rs9425427	1.00[EUR][1000 genomes]
rs9425735	1.00[EUR][1000 genomes]
rs9425768	1.00[EUR][1000 genomes]
rs997165	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916960	chr1:173907804-174080248	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv872551	chr1:173913804-174025660	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv831937	chr1:173949373-174131463	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173942200-173986200	Weak transcription	Fetal Brain Male	brain
2	chr1:173958600-173987200	Weak transcription	Gastric	stomach
3	chr1:173962000-173988400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:173962200-173984200	Weak transcription	Primary T cells from cord blood	blood
5	chr1:173962200-173989000	Weak transcription	Fetal Kidney	kidney
6	chr1:173962200-173989600	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:173962200-173989600	Weak transcription	Aorta	Aorta
8	chr1:173962200-173989800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:173962200-173990400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:173962400-173987800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:173962600-173986000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:173962600-173988400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:173962600-173988600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:173962600-173989400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:173962800-173989800	Weak transcription	Placenta	Placenta
16	chr1:173965000-173989600	Weak transcription	Fetal Thymus	thymus
17	chr1:173965200-173986600	Weak transcription	HUVEC	blood vessel
18	chr1:173966200-173986200	Weak transcription	Fetal Brain Female	brain
19	chr1:173966200-173989800	Weak transcription	Fetal Muscle Leg	muscle
20	chr1:173966400-173986600	Weak transcription	Thymus	Thymus
21	chr1:173966400-173987800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:173966400-173989600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:173966400-173989800	Weak transcription	Esophagus	oesophagus
24	chr1:173967800-173987600	Weak transcription	Brain Germinal Matrix	brain
25	chr1:173968400-173987200	Weak transcription	Fetal Intestine Large	intestine
26	chr1:173971200-173988400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:173974600-173986400	Weak transcription	HSMM	muscle
28	chr1:173975000-173984000	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:173975000-173986400	Weak transcription	HMEC	breast
30	chr1:173975200-173986000	Weak transcription	Dnd41	blood
31	chr1:173975200-173987200	Weak transcription	NHLF	lung
32	chr1:173975400-173987200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr1:173975600-173986000	Weak transcription	Adipose Nuclei	Adipose
34	chr1:173975600-173986200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr1:173975800-173986400	Weak transcription	NHDF-Ad	bronchial
36	chr1:173976600-173990000	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:173976800-173986400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:173977000-173984800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:173977000-173986400	Weak transcription	Fetal Stomach	stomach
40	chr1:173977200-173986400	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr1:173977200-173989200	Weak transcription	NH-A	brain
42	chr1:173977800-173987200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:173977800-173988400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:173978600-173984000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:173978600-173985600	Weak transcription	Colonic Mucosa	Colon
46	chr1:173978600-173986000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:173978600-173986000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr1:173978600-173986000	Weak transcription	GM12878-XiMat	blood
49	chr1:173978600-173986600	Weak transcription	Hela-S3	cervix
50	chr1:173978600-173989200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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