Variant report

Variant	rs9658584
Chromosome Location	chr1:86047311-86047312
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	RAD21	chr1:86045705-86047615	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr1:86045710-86047578	Hela-S3	cervix:	n/a	chr1:86047350-86047360 chr1:86045792-86045801
3	STAT3	chr1:86047256-86047526	MCF10A-Er-Src	breast:	n/a	n/a
4	RAD21	chr1:86046984-86047571	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:86045313-86051202	ProgFib	skin:	n/a	n/a
6	POLR2A	chr1:86041793-86051199	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:86046260-86050835	HepG2	liver:	n/a	n/a
8	YY1	chr1:86046968-86047453	SK-N-SH_RA	brain:	n/a	n/a
9	TEAD4	chr1:86045890-86051052	ECC-1	luminal epithelium:	n/a	n/a
10	SMC3	chr1:86045729-86047898	Hela-S3	cervix:	n/a	n/a
11	TAL1	chr1:86046321-86047375	K562	blood:	n/a	n/a
12	ATF2	chr1:86045932-86051178	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr1:86045953-86047678	SK-N-SH	brain:	n/a	n/a
14	JUND	chr1:86046072-86051121	SK-N-SH	brain:	n/a	chr1:86047323-86047335 chr1:86046521-86046530 chr1:86048309-86048318
15	REST	chr1:86045904-86047373	PANC-1	pancreas:	n/a	chr1:86046314-86046324
16	TAF1	chr1:86045685-86048404	H1-hESC	embryonic stem cell:	n/a	n/a
17	NFIC	chr1:86046816-86047590	SK-N-SH	brain:	n/a	n/a
18	RAD21	chr1:86046754-86047370	MCF-7	breast:	n/a	n/a
19	REST	chr1:86046193-86047379	SK-N-SH	brain:	n/a	chr1:86046314-86046324
20	CTCF	chr1:86047240-86047390	HAc	cerebellar:	n/a	n/a
21	TBP	chr1:86045223-86048449	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:86045842-86049091	Hela-S3	cervix:	n/a	n/a
23	RAD21	chr1:86046062-86048820	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr1:86046072-86049245	HUVEC	blood vessel:	n/a	n/a
25	NFIC	chr1:86045561-86049147	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr1:86045919-86047354	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr1:86041833-86052222	HUVEC	blood vessel:	n/a	n/a
28	CHD2	chr1:86045850-86047554	Hela-S3	cervix:	n/a	chr1:86046866-86046876 chr1:86046027-86046037
29	STAT3	chr1:86047260-86047552	Hela-S3	cervix:	n/a	n/a
30	SIN3AK20	chr1:86046022-86049217	SK-N-SH	brain:	n/a	n/a
31	RAD21	chr1:86045965-86047403	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr1:86046879-86047334	MCF-7	breast:	n/a	n/a
33	POLR2A	chr1:86047199-86047532	U87	brain:	n/a	n/a
34	E2F4	chr1:86047059-86047368	MCF10A-Er-Src	breast:	n/a	chr1:86047277-86047288
35	TCF12	chr1:86045933-86048970	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr1:86041771-86051250	HUVEC	blood vessel:	n/a	n/a
37	GATA3	chr1:86045616-86047524	A549	lung:	n/a	chr1:86046062-86046071
38	E2F1	chr1:86046120-86047385	Hela-S3	cervix:	n/a	chr1:86046524-86046533 chr1:86046431-86046441 chr1:86047277-86047288 chr1:86046564-86046573
39	POLR2A	chr1:86046076-86049278	Hela-S3	cervix:	n/a	n/a
40	GTF2F1	chr1:86047072-86048453	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr1:86046027-86047507	PFSK-1	brain:	n/a	n/a
42	CHD1	chr1:86041753-86052318	IMR90	lung:	n/a	chr1:86046866-86046876 chr1:86046027-86046037 chr1:86044526-86044536
43	RAD21	chr1:86046822-86047367	MCF-7	breast:	n/a	n/a
44	SMARCC1	chr1:86045796-86047730	Hela-S3	cervix:	n/a	n/a
45	SP1	chr1:86046098-86049347	H1-hESC	embryonic stem cell:	n/a	chr1:86047281-86047288 chr1:86046772-86046786 chr1:86046866-86046875
46	FOSL2	chr1:86047087-86047639	A549	lung:	n/a	chr1:86047323-86047335
47	POLR2A	chr1:86046113-86049066	ECC-1	luminal epithelium:	n/a	n/a
48	MXI1	chr1:86045681-86047893	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr1:86046115-86050994	A549	lung:	n/a	n/a
50	MAX	chr1:86045774-86049318	Hela-S3	cervix:	n/a	chr1:86046475-86046485

No.	Distal block	Cell Line	Cell type
1	chr1:86046008..86048463-chr1:86063364..86065472,5	MCF-7	breast:
2	chr1:86046059..86047966-chr1:86055986..86059242,3	MCF-7	breast:
3	chr1:86045233..86051336-chr1:86057804..86069814,19	K562	blood:
4	chr1:86043660..86051626-chr1:86167839..86177430,17	K562	blood:
5	chr1:85930091..85932037-chr1:86045511..86048058,4	MCF-7	breast:
6	chr1:86046915..86048660-chr1:86125105..86127128,2	K562	blood:
7	chr1:85958709..85962572-chr1:86044730..86049172,10	MCF-7	breast:
8	chr1:85959814..85963220-chr1:86043447..86048399,5	MCF-7	breast:
9	chr1:85927983..85931587-chr1:86046693..86050651,4	MCF-7	breast:
10	chr1:86046116..86050935-chr1:86168336..86177340,12	K562	blood:
11	chr1:85740856..85742558-chr1:86046586..86048600,2	MCF-7	breast:
12	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
13	chr1:86043937..86050216-chr1:86058297..86066765,12	K562	blood:
14	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:
15	chr1:85809656..85810579-chr1:86046914..86047542,3	MCF-7	breast:

Variant related genes	Relation type
DDAH1	TF binding region
ENSG00000272691	TF binding region
ENSG00000117174	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000153904	Chromatin interaction
ENSG00000199934	Chromatin interaction
ENSG00000142867	Chromatin interaction
ENSG00000230285	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12566318	0.88[CEU][hapmap];0.85[AFR][1000 genomes]
rs2297138	0.94[CEU][hapmap];0.82[TSI][hapmap];0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2297139	0.94[CEU][hapmap];0.85[TSI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs55679600	0.85[AFR][1000 genomes]
rs55750909	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs6659670	0.85[AFR][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 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	chr1:86041800-86047800	Active TSS	Aorta	Aorta
2	chr1:86045200-86047400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:86045200-86047600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:86045200-86047600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:86045200-86048600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:86045400-86047600	Active TSS	Colon Smooth Muscle	Colon
7	chr1:86045400-86047800	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:86045400-86047800	Active TSS	Ovary	ovary
9	chr1:86045400-86048000	Active TSS	Rectal Smooth Muscle	rectum
10	chr1:86045400-86048600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:86045400-86048800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:86045600-86047400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:86045600-86047400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:86045600-86047400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:86045600-86047400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr1:86045600-86047400	Active TSS	HSMM	muscle
17	chr1:86045600-86047600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:86045600-86047600	Active TSS	Duodenum Mucosa	Duodenum
19	chr1:86045600-86047600	Active TSS	Psoas Muscle	Psoas
20	chr1:86045600-86047800	Active TSS	Fetal Kidney	kidney
21	chr1:86045600-86048000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:86045600-86048200	Active TSS	Right Ventricle	heart
23	chr1:86045800-86047400	Bivalent/Poised TSS	Sigmoid Colon	Sigmoid Colon
24	chr1:86045800-86047600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:86045800-86047600	Active TSS	Left Ventricle	heart
26	chr1:86045800-86047800	Active TSS	Brain Substantia Nigra	brain
27	chr1:86045800-86048200	Active TSS	Brain Angular Gyrus	brain
28	chr1:86045800-86048400	Active TSS	Brain Cingulate Gyrus	brain
29	chr1:86045800-86048400	Active TSS	Lung	lung
30	chr1:86045800-86048400	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr1:86046000-86047400	Active TSS	Hela-S3	cervix
32	chr1:86046000-86047400	Active TSS	K562	blood
33	chr1:86046000-86047600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:86046000-86047600	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr1:86046000-86047600	Active TSS	Liver	Liver
36	chr1:86046000-86047600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr1:86046000-86047600	Active TSS	Fetal Intestine Large	intestine
38	chr1:86046000-86047600	Active TSS	Pancreas	Pancrea
39	chr1:86046000-86047600	Active TSS	Placenta Amnion	Placenta Amnion
40	chr1:86046000-86047800	Active TSS	Fetal Stomach	stomach
41	chr1:86046000-86048200	Active TSS	Right Atrium	heart
42	chr1:86046200-86047400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr1:86046200-86047400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr1:86046200-86047400	Active TSS	Adipose Nuclei	Adipose
45	chr1:86046200-86047800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr1:86046200-86047800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:86046200-86047800	Active TSS	Gastric	stomach
48	chr1:86046600-86047400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr1:86046600-86047400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:86046600-86048000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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