Variant report

Variant	rs859013
Chromosome Location	chr1:158151218-158151219
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr1:158149957-158151347	HEK293-T-REx	kidney:	n/a	n/a
2	POLR2A	chr1:158150612-158151406	H1-neurons	neurons:	n/a	n/a
3	SIN3A	chr1:158150172-158151486	H1-hESC	embryonic stem cell:	n/a	chr1:158150984-158150995 chr1:158151194-158151207
4	CTBP2	chr1:158150605-158151546	H1-hESC	embryonic stem cell:	n/a	n/a
5	MAX	chr1:158150990-158151573	H1-hESC	embryonic stem cell:	n/a	n/a
6	KAP1	chr1:158150127-158151579	HEK293	kidney:	n/a	n/a
7	MYC	chr1:158150383-158151586	NB4	blood:	n/a	n/a
8	TBP	chr1:158150531-158151452	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr1:158150628-158151278	H1-hESC	embryonic stem cell:	n/a	n/a
10	MAX	chr1:158150387-158151365	NB4	blood:	n/a	n/a
11	POLR2A	chr1:158150572-158151511	H1-neurons	neurons:	n/a	n/a
12	BACH1	chr1:158150940-158151285	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr1:158148912-158153430	K562	blood:	n/a	n/a
14	ELF1	chr1:158150430-158151577	GM12878	blood:	n/a	chr1:158150602-158150613
15	MAX	chr1:158150654-158151590	H1-hESC	embryonic stem cell:	n/a	n/a
16	REST	chr1:158150361-158151255	H1-neurons	neurons:	n/a	chr1:158151098-158151111 chr1:158150685-158150698 chr1:158150685-158150698 chr1:158151194-158151207
17	ZNF143	chr1:158150671-158151491	H1-hESC	embryonic stem cell:	n/a	chr1:158151097-158151115

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:158151204-158151254	NH-A	brain:	n/a
2	chr1:158151204-158151254	NB4	blood:	n/a
3	chr1:158151204-158151254	NHDF-neo	bronchial:	n/a
4	chr1:158151204-158151254	K562	blood:	n/a
5	chr1:158151204-158151254	GM12892	blood:	n/a
6	chr1:158151204-158151254	IMR90	lung:	fetal
7	chr1:158151204-158151254	HCM	heart:	n/a
8	chr1:158151204-158151254	HCF	heart:	n/a
9	chr1:158151204-158151254	SK-N-MC	brain:	n/a
10	chr1:158151204-158151254	T-47D	breast:	n/a
11	chr1:158151204-158151254	PrEC	prostate:	n/a
12	chr1:158151204-158151254	HRE	kidney:	n/a
13	chr1:158151204-158151254	AG09319	gingival:	n/a
14	chr1:158151204-158151254	ovcar-3	ovarian:	n/a
15	chr1:158151204-158151254	HIPEpiC	eye:	n/a
16	chr1:158151204-158151254	HEEpiC	esophagus:	n/a
17	chr1:158151204-158151254	NHBE	bronchial:	n/a
18	chr1:158151204-158151254	HPAEpiC	pulmonary alveolar:	n/a
19	chr1:158151204-158151254	GM12878	blood:	n/a
20	chr1:158151204-158151254	SAEC	small airway:	n/a
21	chr1:158151204-158151254	U87	brain:	n/a
22	chr1:158151204-158151254	A549	lung:	n/a
23	chr1:158151204-158151254	HNPCEpiC	eye:	n/a
24	chr1:158151204-158151254	Jurkat	blood:	n/a
25	chr1:158151204-158151254	AG09309	skin:	n/a
26	chr1:158151204-158151254	HAEpiC	amniotic membrane:	n/a
27	chr1:158151204-158151254	BE2_C	brain:	n/a
28	chr1:158151204-158151254	AoSMC	blood vessel:	n/a
29	chr1:158151204-158151254	GM19239	blood:	n/a
30	chr1:158151204-158151254	HL-60	blood:	n/a
31	chr1:158151204-158151254	HUVEC	blood vessel:	n/a
32	chr1:158151204-158151254	Hepatocyte	liver:	n/a
33	chr1:158151204-158151254	ProgFib	skin:	n/a
34	chr1:158151204-158151254	AG10803	skin:	n/a
35	chr1:158151204-158151254	RPTEC	kidney:	n/a
36	chr1:158151204-158151254	MCF10A-Er-Src	breast:	n/a
37	chr1:158151204-158151254	GM12891	blood:	n/a
38	chr1:158151204-158151254	HMEC	breast:	n/a
39	chr1:158151204-158151254	PFSK-1	brain:	n/a
40	chr1:158151204-158151254	NT2-D1	testis:	n/a
41	chr1:158151204-158151254	BJ	skin:	n/a
42	chr1:158151204-158151254	GM06990	blood:	n/a
43	chr1:158151204-158151254	AG04450	lung:	fetal
44	chr1:158151204-158151254	SK-N-SH_RA	brain:	n/a
45	chr1:158151204-158151254	HCT-116	colon:	n/a
46	chr1:158151204-158151254	Caco-2	colon:	n/a
47	chr1:158151204-158151254	ECC-1	luminal epithelium:	n/a
48	chr1:158151204-158151254	SK-N-SH	brain:	n/a
49	chr1:158151204-158151254	Hela-S3	cervix:	n/a
50	chr1:158151204-158151254	HepG2	liver:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158149755..158153217-chr1:158153415..158155911,3	K562	blood:

No data

Variant related genes	Relation type
ELL2P1	TF binding region
ELL2P1	CpG island

Extended variants
information (count: 58 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10489821	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10489823	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12040592	0.91[CEU][hapmap]
rs12723141	0.95[JPT][hapmap]
rs1570699	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1633141	0.92[CEU][hapmap]
rs1633149	0.92[CEU][hapmap]
rs16839951	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1748383	0.92[CEU][hapmap]
rs1748387	0.92[CEU][hapmap]
rs1980757	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2518477	0.92[CEU][hapmap]
rs3021476	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3021478	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3087210	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3087211	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3087212	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3087213	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3118165	0.92[CEU][hapmap]
rs368130	0.92[CEU][hapmap]
rs374513	0.92[CEU][hapmap]
rs377795	0.92[CEU][hapmap]
rs383688	0.92[CEU][hapmap]
rs384414	0.92[CEU][hapmap]
rs389495	0.91[CEU][hapmap]
rs393304	0.84[CEU][hapmap]
rs401904	0.92[CEU][hapmap]
rs402699	0.92[CEU][hapmap]
rs407309	0.92[CEU][hapmap]
rs413557	0.92[CEU][hapmap]
rs434570	0.92[CEU][hapmap]
rs440862	0.92[CEU][hapmap]
rs448005	0.92[CEU][hapmap]
rs448556	0.92[CEU][hapmap]
rs449838	0.92[CEU][hapmap]
rs594364	0.92[CEU][hapmap]
rs607948	0.92[CEU][hapmap]
rs623215	0.92[CEU][hapmap]
rs6692064	0.92[EUR][1000 genomes]
rs6692133	0.92[EUR][1000 genomes]
rs691077	0.81[CEU][hapmap]
rs691175	0.92[CEU][hapmap]
rs691551	0.92[CEU][hapmap]
rs72711995	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72711999	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7530662	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs7548147	1.00[JPT][hapmap]
rs7556487	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs859001	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs859002	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859003	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859005	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859008	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859009	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859010	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859011	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs859013	SHE	cis	cerebellum	SCAN
rs859013	NCSTN	cis	cerebellum	SCAN
rs859013	CD1A	cis	cerebellum	SCAN
rs859013	VHLL	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158149200-158152400	Flanking Active TSS	Primary B cells from cord blood	blood
2	chr1:158150000-158151600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:158150000-158151600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
4	chr1:158150200-158151400	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:158150200-158151600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:158150200-158151600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
7	chr1:158150200-158151800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:158150400-158151400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:158150400-158151400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr1:158150400-158151400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:158150400-158151400	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
12	chr1:158150400-158151400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr1:158150400-158151400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr1:158150400-158151400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
15	chr1:158150400-158151600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
16	chr1:158150400-158151600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:158150400-158151600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:158150400-158151600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:158150400-158151600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
20	chr1:158150400-158151600	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:158150400-158151600	Bivalent/Poised TSS	Fetal Brain Female	brain
22	chr1:158150400-158151600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
23	chr1:158150400-158151600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
24	chr1:158150400-158151600	Flanking Active TSS	HMEC	breast
25	chr1:158150400-158151800	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr1:158150600-158151400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
27	chr1:158150600-158151400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:158150600-158151400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:158150600-158151400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
30	chr1:158150600-158151400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr1:158150600-158151400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
32	chr1:158150600-158151400	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:158150600-158151400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr1:158150600-158151400	Active TSS	Primary monocytes fromperipheralblood	blood
35	chr1:158150600-158151400	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr1:158150600-158151400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:158150600-158151400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:158150600-158151400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:158150600-158151400	Flanking Active TSS	Colonic Mucosa	Colon
40	chr1:158150600-158151400	Active TSS	Fetal Heart	heart
41	chr1:158150600-158151400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
42	chr1:158150600-158151400	Active TSS	Fetal Kidney	kidney
43	chr1:158150600-158151400	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
44	chr1:158150600-158151400	Flanking Bivalent TSS/Enh	Placenta	Placenta
45	chr1:158150600-158151400	Flanking Active TSS	Pancreas	Pancrea
46	chr1:158150600-158151400	Bivalent/Poised TSS	HSMMtube	muscle
47	chr1:158150600-158151400	Bivalent/Poised TSS	NH-A	brain
48	chr1:158150600-158151600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:158150600-158151600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:158150600-158151600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood

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