Variant report

Variant	rs11587899
Chromosome Location	chr1:180895528-180895529
allele	C/G
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	CTCF	chr1:180895440-180895590	AoAF	blood vessel:	n/a	n/a
2	EP300	chr1:180895348-180896081	SK-N-SH_RA	brain:	n/a	n/a
3	TAF1	chr1:180895258-180896187	H1-neurons	neurons:	n/a	n/a
4	REST	chr1:180895315-180896250	H1-neurons	neurons:	n/a	n/a
5	EP300	chr1:180894092-180899177	SK-N-SH	brain:	n/a	chr1:180896188-180896202
6	ESR1	chr1:180895253-180895625	ECC-1	luminal epithelium:	n/a	chr1:180895448-180895465
7	REST	chr1:180895055-180896618	H1-neurons	neurons:	n/a	chr1:180896323-180896337 chr1:180896327-180896340 chr1:180896323-180896343 chr1:180896323-180896343
8	CTCF	chr1:180895500-180895650	BE2_C	brain:	n/a	n/a
9	EP300	chr1:180895362-180896084	SK-N-SH_RA	brain:	n/a	n/a
10	GATA1	chr1:180895362-180896123	PBDE	blood:	n/a	n/a
11	POLR2A	chr1:180895517-180896058	SK-N-MC	brain:	n/a	n/a
12	CTCF	chr1:180895420-180895570	SK-N-SH_RA	brain:	n/a	n/a
13	TAL1	chr1:180895412-180896071	K562	blood:	n/a	n/a
14	ZNF384	chr1:180895386-180895971	K562	blood:	n/a	n/a
15	ZNF263	chr1:180894869-180896749	K562	blood:	n/a	n/a
16	CTCF	chr1:180895460-180895610	NHDF-neo	bronchial:	n/a	n/a
17	POLR2A	chr1:180895261-180896458	H1-neurons	neurons:	n/a	n/a
18	YY1	chr1:180895479-180896037	SK-N-SH_RA	brain:	n/a	chr1:180896003-180896014
19	GATA2	chr1:180894667-180896194	SH-SY5Y	brain:	n/a	n/a
20	REST	chr1:180895357-180896069	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr1:180895285-180896202	H1-neurons	neurons:	n/a	n/a
22	TCF12	chr1:180895271-180896273	SK-N-SH	brain:	n/a	chr1:180896135-180896145

No.	Distal block	Cell Line	Cell type
1	chr1:180894020..180896970-chr1:180921543..180923993,2	MCF-7	breast:
2	chr1:180892738..180895948-chr1:181056431..181059504,3	K562	blood:
3	chr1:180888347..180891443-chr1:180893391..180896382,5	K562	blood:
4	chr1:180879805..180882226-chr1:180894957..180896873,2	MCF-7	breast:
5	chr1:180893588..180895646-chr1:181053051..181055501,3	MCF-7	breast:
6	chr1:180891831..180893938-chr1:180895346..180897268,3	K562	blood:
7	chr1:180865980..180867777-chr1:180893565..180896342,2	K562	blood:

Variant related genes	Relation type
KIAA1614	TF binding region
ENSG00000162783	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11581837	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11582550	0.85[EUR][1000 genomes]
rs11584360	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12735084	0.96[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12748054	0.96[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12753478	0.92[CEU][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13374657	0.92[AMR][1000 genomes];0.91[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	nsv1014404	chr1:180770155-181090200	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv872579	chr1:180881148-180931508	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1001918	chr1:180886750-180908005	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180886000-180911000	Enhancers	Fetal Thymus	thymus
2	chr1:180887600-180915800	Weak transcription	Osteobl	bone
3	chr1:180888400-180897600	Weak transcription	Aorta	Aorta
4	chr1:180888600-180917200	Weak transcription	Gastric	stomach
5	chr1:180890400-180895600	Enhancers	Thymus	Thymus
6	chr1:180890400-180898200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:180890600-180898000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:180890800-180898200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:180890800-180898600	Enhancers	Placenta	Placenta
10	chr1:180891000-180897800	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:180891400-180896600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:180891600-180901000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:180891800-180898200	Enhancers	Fetal Muscle Trunk	muscle
14	chr1:180893000-180895600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr1:180893000-180896600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr1:180893000-180897400	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:180893000-180897400	Weak transcription	Lung	lung
18	chr1:180893000-180897800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:180893000-180898000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:180893200-180896800	Enhancers	K562	blood
21	chr1:180893600-180895600	Weak transcription	NHEK	skin
22	chr1:180893600-180897800	Enhancers	Fetal Muscle Leg	muscle
23	chr1:180894000-180895600	Weak transcription	NH-A	brain
24	chr1:180894000-180897800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:180894200-180895600	Enhancers	Brain Germinal Matrix	brain
26	chr1:180894200-180895800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr1:180894200-180896400	Enhancers	Spleen	Spleen
28	chr1:180894200-180896600	Enhancers	Fetal Brain Male	brain
29	chr1:180894200-180897000	Flanking Active TSS	HepG2	liver
30	chr1:180894200-180897200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr1:180894200-180897400	Enhancers	Primary hematopoietic stem cells	blood
32	chr1:180894200-180897800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:180894200-180898000	Enhancers	Fetal Heart	heart
34	chr1:180894200-180898000	Enhancers	Fetal Lung	lung
35	chr1:180894200-180898000	Enhancers	Fetal Stomach	stomach
36	chr1:180894200-180898200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:180894200-180898600	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr1:180894200-180899000	Enhancers	Left Ventricle	heart
39	chr1:180894400-180895600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:180894400-180896400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:180894400-180896400	Enhancers	Fetal Kidney	kidney
42	chr1:180894400-180896800	Enhancers	Fetal Intestine Small	intestine
43	chr1:180894400-180899000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:180894600-180895600	Enhancers	Fetal Brain Female	brain
45	chr1:180894600-180895800	Enhancers	Duodenum Mucosa	Duodenum
46	chr1:180894600-180896000	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr1:180894600-180896000	Flanking Active TSS	Brain Hippocampus Middle	brain
48	chr1:180894600-180896200	Enhancers	Stomach Mucosa	stomach
49	chr1:180894600-180896400	Enhancers	HSMMtube	muscle
50	chr1:180894600-180896600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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