Variant report

Variant	rs11576789
Chromosome Location	chr1:211817646-211817647
allele	C/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	NFIC	chr1:211816869-211817647	ECC-1	luminal epithelium:	n/a	n/a
2	TCF7L2	chr1:211816599-211817766	Hela-S3	cervix:	n/a	chr1:211817379-211817389 chr1:211816835-211816851 chr1:211816835-211816851 chr1:211816839-211816848
3	POLR2A	chr1:211815491-211817685	Hela-S3	cervix:	n/a	n/a
4	STAT1	chr1:211816244-211817683	Hela-S3	cervix:	n/a	chr1:211817011-211817023 chr1:211817319-211817327 chr1:211817317-211817328 chr1:211817577-211817588
5	BRCA1	chr1:211817084-211817649	Hela-S3	cervix:	n/a	n/a
6	MAX	chr1:211816621-211817674	Hela-S3	cervix:	n/a	chr1:211816943-211816952
7	MYC	chr1:211816792-211817758	MCF10A-Er-Src	breast:	n/a	chr1:211816943-211816952
8	MAFK	chr1:211816606-211817654	Hela-S3	cervix:	n/a	n/a
9	CTCF	chr1:211817297-211817700	K562	blood:	n/a	chr1:211817530-211817548 chr1:211817532-211817545
10	MXI1	chr1:211816713-211817810	SK-N-SH	brain:	n/a	n/a
11	NFIC	chr1:211816719-211817754	SK-N-SH	brain:	n/a	n/a
12	CTCF	chr1:211817520-211817670	BE2_C	brain:	n/a	chr1:211817530-211817548 chr1:211817532-211817545
13	MAX	chr1:211816966-211817650	K562	blood:	n/a	n/a
14	MYC	chr1:211816791-211817714	MCF10A-Er-Src	breast:	n/a	chr1:211816943-211816952

No.	Distal block	Cell Line	Cell type
1	chr1:211816612..211818942-chr1:211819387..211821012,2	MCF-7	breast:
2	chr1:211750794..211754252-chr1:211815868..211819773,4	MCF-7	breast:
3	chr1:211749200..211754595-chr1:211816014..211824648,8	K562	blood:

Variant related genes	Relation type
ENSG00000228792	TF binding region
ENSG00000170385	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10158305	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10158307	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10158309	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10158749	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10158790	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10158874	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10159253	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10779564	0.87[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs10779565	0.81[EUR][1000 genomes]
rs10779566	0.81[EUR][1000 genomes]
rs10863919	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs10863920	0.83[EUR][1000 genomes]
rs11119780	0.81[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs11119783	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11119785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119787	0.85[EUR][1000 genomes]
rs11577255	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123429	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs12142250	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12727505	0.85[EUR][1000 genomes]
rs12734494	0.87[ASN][1000 genomes]
rs12741252	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs12744873	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12758005	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1373293	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34451435	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35531215	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4245741	0.81[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs4951539	0.80[CEU][hapmap]
rs61851777	0.80[EUR][1000 genomes]
rs6540698	0.80[EUR][1000 genomes]
rs6667179	0.82[JPT][hapmap]
rs6669878	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6670986	0.81[CEU][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs6671497	0.81[EUR][1000 genomes]
rs6693364	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7523748	0.81[CEU][hapmap];0.85[TSI][hapmap]
rs7525247	0.82[JPT][hapmap]
rs7551699	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs894853	0.81[CEU][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs894854	0.80[EUR][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	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211811400-211829600	Enhancers	Fetal Intestine Small	intestine
2	chr1:211811600-211828200	Enhancers	Fetal Intestine Large	intestine
3	chr1:211813600-211821600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:211813800-211822600	Weak transcription	NHDF-Ad	bronchial
5	chr1:211814600-211818600	Flanking Active TSS	Hela-S3	cervix
6	chr1:211816000-211818000	Enhancers	Fetal Thymus	thymus
7	chr1:211816000-211818400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr1:211816200-211817800	Flanking Active TSS	HepG2	liver
9	chr1:211816200-211818600	Enhancers	Duodenum Mucosa	Duodenum
10	chr1:211816200-211819400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:211816400-211817800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr1:211816400-211817800	Enhancers	HMEC	breast
13	chr1:211816400-211817800	Enhancers	K562	blood
14	chr1:211816600-211817800	Enhancers	Right Ventricle	heart
15	chr1:211816600-211818400	Enhancers	Adipose Nuclei	Adipose
16	chr1:211816600-211818800	Enhancers	Liver	Liver
17	chr1:211816800-211817800	Enhancers	NHLF	lung
18	chr1:211817000-211817800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:211817000-211817800	Enhancers	Fetal Stomach	stomach
20	chr1:211817200-211821200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:211817400-211818400	Weak transcription	Fetal Brain Female	brain
22	chr1:211817400-211818400	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:211817400-211827000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:211817400-211827400	Weak transcription	Fetal Heart	heart
25	chr1:211817600-211817800	Enhancers	Primary T cells from cord blood	blood
26	chr1:211817600-211817800	Enhancers	A549	lung
27	chr1:211817600-211818600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:211817600-211818800	Weak transcription	Osteobl	bone
29	chr1:211817600-211819600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:211817600-211819600	Weak transcription	HUVEC	blood vessel
31	chr1:211817600-211821000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:211817600-211821000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:211817600-211821000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:211817600-211821200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:211817600-211821200	Weak transcription	Brain Anterior Caudate	brain
36	chr1:211817600-211821200	Weak transcription	Colonic Mucosa	Colon
37	chr1:211817600-211821200	Weak transcription	Esophagus	oesophagus
38	chr1:211817600-211821200	Weak transcription	Placenta	Placenta
39	chr1:211817600-211821200	Weak transcription	Pancreas	Pancrea
40	chr1:211817600-211821200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:211817600-211821200	Weak transcription	Stomach Mucosa	stomach
42	chr1:211817600-211821800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:211817600-211823000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:211817600-211823200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:211817600-211826800	Weak transcription	Gastric	stomach
46	chr1:211817600-211827000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:211817600-211830600	Weak transcription	Right Atrium	heart

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