Variant report

Variant	rs2911571
Chromosome Location	chr1:85156821-85156822
allele	A/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	MTA3	chr1:85156135-85157003	GM12878	blood:	n/a	n/a
2	RCOR1	chr1:85155565-85157119	K562	blood:	n/a	n/a
3	POLR2A	chr1:85155514-85156955	GM19193	blood:	n/a	n/a
4	MXI1	chr1:85155519-85156836	GM12878	blood:	n/a	chr1:85156629-85156638
5	CHD2	chr1:85155640-85156898	H1-hESC	embryonic stem cell:	n/a	chr1:85156471-85156481 chr1:85156140-85156150
6	POLR2A	chr1:85155705-85157191	GM12891	blood:	n/a	n/a
7	POLR2A	chr1:85155921-85156874	PFSK-1	brain:	n/a	n/a
8	POLR2A	chr1:85155745-85156892	NB4	blood:	n/a	n/a
9	HCFC1	chr1:85154848-85156890	Hela-S3	cervix:	n/a	n/a
10	NFYB	chr1:85155996-85156854	K562	blood:	n/a	chr1:85156273-85156288
11	NRF1	chr1:85156095-85156900	SK-N-SH	brain:	n/a	chr1:85156473-85156482 chr1:85156413-85156424
12	POLR2A	chr1:85155560-85156916	GM18526	blood:	n/a	n/a
13	NFYA	chr1:85156089-85156856	Hela-S3	cervix:	n/a	n/a
14	MAX	chr1:85155454-85156833	HepG2	liver:	n/a	chr1:85156630-85156639 chr1:85155690-85155699 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85155505-85155514 chr1:85156629-85156639
15	MAX	chr1:85156278-85157199	H1-hESC	embryonic stem cell:	n/a	chr1:85156630-85156639 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85156629-85156639
16	IRF1	chr1:85156095-85157409	K562	blood:	n/a	chr1:85156469-85156483 chr1:85156608-85156620 chr1:85156180-85156194 chr1:85157134-85157147 chr1:85157134-85157147 chr1:85157134-85157147
17	CTCF	chr1:85155022-85156917	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr1:85155576-85156924	GM18505	blood:	n/a	n/a
19	POLR2A	chr1:85155218-85156917	K562	blood:	n/a	n/a
20	POLR2A	chr1:85155540-85156984	ECC-1	luminal epithelium:	n/a	n/a
21	MYC	chr1:85155275-85157548	K562	blood:	n/a	chr1:85156630-85156639 chr1:85155690-85155699 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85155505-85155514 chr1:85156629-85156639
22	SMARCB1	chr1:85155440-85156950	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:85153889-85157405	K562	blood:	n/a	n/a
24	REST	chr1:85155375-85156853	H1-neurons	neurons:	n/a	chr1:85156064-85156074 chr1:85155820-85155833 chr1:85155784-85155797 chr1:85156110-85156130 chr1:85155694-85155712
25	MXI1	chr1:85156103-85157067	K562	blood:	n/a	chr1:85156629-85156638
26	MAX	chr1:85155430-85156878	H1-hESC	embryonic stem cell:	n/a	chr1:85156630-85156639 chr1:85155690-85155699 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85155505-85155514 chr1:85156629-85156639
27	MYC	chr1:85155245-85157349	K562	blood:	n/a	chr1:85156630-85156639 chr1:85155690-85155699 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85155505-85155514 chr1:85156629-85156639
28	MYC	chr1:85156024-85157078	A549	lung:	n/a	chr1:85156630-85156639 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85156629-85156639
29	STAT5A	chr1:85156443-85156872	GM12878	blood:	n/a	n/a
30	RUNX3	chr1:85155986-85156960	GM12878	blood:	n/a	n/a
31	POLR2A	chr1:85156772-85156857	HepG2	liver:	n/a	n/a
32	MAX	chr1:85156242-85157015	MCF-7	breast:	n/a	chr1:85156630-85156639 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85156629-85156639
33	POLR2A	chr1:85156217-85156920	H1-hESC	embryonic stem cell:	n/a	n/a
34	JUND	chr1:85155439-85156859	K562	blood:	n/a	chr1:85156446-85156457 chr1:85156273-85156282
35	POLR2A	chr1:85155367-85156833	K562	blood:	n/a	n/a
36	MAX	chr1:85156142-85156914	A549	lung:	n/a	chr1:85156630-85156639 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85156629-85156639
37	POLR2A	chr1:85155396-85156852	HL-60	blood:	n/a	n/a
38	SP1	chr1:85156049-85156821	H1-hESC	embryonic stem cell:	n/a	chr1:85156174-85156188 chr1:85156472-85156481 chr1:85156183-85156192 chr1:85156473-85156486 chr1:85156471-85156483 chr1:85156472-85156481 chr1:85156182-85156194 chr1:85156473-85156482 chr1:85156471-85156483 chr1:85156184-85156193 chr1:85156471-85156482 chr1:85156183-85156192 chr1:85156472-85156486
39	MXI1	chr1:85155060-85157133	IMR90	lung:	n/a	chr1:85156629-85156638
40	POLR2A	chr1:85155678-85156892	PFSK-1	brain:	n/a	n/a
41	MAX	chr1:85155394-85157049	SK-N-SH	brain:	n/a	chr1:85156630-85156639 chr1:85155690-85155699 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85155505-85155514 chr1:85156629-85156639
42	MAX	chr1:85155144-85156868	Hela-S3	cervix:	n/a	chr1:85156630-85156639 chr1:85155690-85155699 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85155505-85155514 chr1:85156629-85156639
43	TEAD4	chr1:85156192-85156985	K562	blood:	n/a	n/a
44	TCF12	chr1:85155517-85156835	ECC-1	luminal epithelium:	n/a	n/a
45	CHD1	chr1:85156596-85157143	H1-hESC	embryonic stem cell:	n/a	n/a
46	CREB1	chr1:85155586-85156840	K562	blood:	n/a	n/a
47	POLR2A	chr1:85154104-85156954	K562	blood:	n/a	n/a
48	E2F6	chr1:85155524-85156990	H1-hESC	embryonic stem cell:	n/a	chr1:85156141-85156153 chr1:85155820-85155830 chr1:85156473-85156482 chr1:85156470-85156482
49	MYC	chr1:85155432-85157450	K562	blood:	n/a	chr1:85156630-85156639 chr1:85155690-85155699 chr1:85156631-85156638 chr1:85156630-85156639 chr1:85155505-85155514 chr1:85156629-85156639
50	UBTF	chr1:85155547-85156890	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:85156797-85156847	GM12892	blood:	n/a
2	chr1:85156797-85156847	HEEpiC	esophagus:	n/a
3	chr1:85156797-85156847	GM19239	blood:	n/a
4	chr1:85156797-85156847	U87	brain:	n/a
5	chr1:85156797-85156847	ovcar-3	ovarian:	n/a
6	chr1:85156797-85156847	H1-hESC	embryonic stem cell:	embryo
7	chr1:85156797-85156847	PrEC	prostate:	n/a
8	chr1:85156797-85156847	HL-60	blood:	n/a
9	chr1:85156797-85156847	GM12878	blood:	n/a
10	chr1:85156797-85156847	SK-N-MC	brain:	n/a
11	chr1:85156797-85156847	HRPEpiC	eye:	n/a
12	chr1:85156797-85156847	AG04449	skin:	fetal
13	chr1:85156797-85156847	NB4	blood:	n/a
14	chr1:85156797-85156847	HRCEpiC	kidney:	n/a
15	chr1:85156797-85156847	Hepatocyte	liver:	n/a
16	chr1:85156797-85156847	SAEC	small airway:	n/a
17	chr1:85156797-85156847	AG10803	skin:	n/a
18	chr1:85156797-85156847	MCF10A-Er-Src	breast:	n/a
19	chr1:85156797-85156847	T-47D	breast:	n/a
20	chr1:85156797-85156847	GM06990	blood:	n/a
21	chr1:85156797-85156847	NHDF-neo	bronchial:	n/a
22	chr1:85156797-85156847	Caco-2	colon:	n/a
23	chr1:85156797-85156847	HCPEpiC	choroid plexus:	n/a
24	chr1:85156797-85156847	RPTEC	kidney:	n/a
25	chr1:85156797-85156847	HPAEpiC	pulmonary alveolar:	n/a
26	chr1:85156797-85156847	ECC-1	luminal epithelium:	n/a
27	chr1:85156797-85156847	A549	lung:	n/a
28	chr1:85156797-85156847	LNCaP	prostate:	n/a
29	chr1:85156797-85156847	HMEC	breast:	n/a
30	chr1:85156797-85156847	SK-N-SH	brain:	n/a
31	chr1:85156797-85156847	HUVEC	blood vessel:	n/a
32	chr1:85156797-85156847	NT2-D1	testis:	n/a
33	chr1:85156797-85156847	ProgFib	skin:	n/a
34	chr1:85156797-85156847	IMR90	lung:	fetal
35	chr1:85156797-85156847	PFSK-1	brain:	n/a
36	chr1:85156797-85156847	GM12891	blood:	n/a
37	chr1:85156797-85156847	AG09309	skin:	n/a
38	chr1:85156797-85156847	K562	blood:	n/a
39	chr1:85156797-85156847	SK-N-SH_RA	brain:	n/a
40	chr1:85156797-85156847	HepG2	liver:	n/a
41	chr1:85156797-85156847	Jurkat	blood:	n/a
42	chr1:85156797-85156847	AG04450	lung:	fetal
43	chr1:85156797-85156847	AG09319	gingival:	n/a
44	chr1:85156797-85156847	CMK	blood:	n/a
45	chr1:85156797-85156847	HNPCEpiC	eye:	n/a
46	chr1:85156797-85156847	MCF-7	breast:	n/a
47	chr1:85156797-85156847	PANC-1	pancreas:	n/a
48	chr1:85156797-85156847	BE2_C	brain:	n/a
49	chr1:85156797-85156847	HRE	kidney:	n/a
50	chr1:85156797-85156847	BJ	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:78469181..78471632-chr1:85154975..85157700,2	K562	blood:
2	chr1:84969596..84972494-chr1:85154864..85156849,3	K562	blood:
3	chr1:85038587..85040484-chr1:85154316..85157145,3	K562	blood:
4	chr1:84970994..84973830-chr1:85154472..85157447,5	K562	blood:
5	chr1:85038984..85041113-chr1:85155645..85157338,2	K562	blood:
6	chr1:85156633..85159408-chr1:85174909..85176958,2	MCF-7	breast:
7	chr1:84542242..84543745-chr1:85154770..85157524,2	K562	blood:

Variant related genes	Relation type
SSX2IP	TF binding region
SSX2IP	CpG island
ENSG00000162616	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000117151	Chromatin interaction
ENSG00000271576	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000273338	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11578078	0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs12022113	0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs12120614	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12123923	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs12125951	0.92[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap]
rs12127432	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1340527	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340528	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2911567	0.92[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2911575	1.00[ASN][1000 genomes]
rs2911578	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911583	0.97[ASN][1000 genomes]
rs2911611	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2943672	1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2994429	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994437	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs2994439	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2994440	0.92[ASN][1000 genomes]
rs2994449	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2994941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2994949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.92[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3096445	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[ASN][1000 genomes]
rs3768238	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3782	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs4390189	1.00[ASN][1000 genomes]
rs4551615	1.00[ASN][1000 genomes]
rs56681543	0.98[ASN][1000 genomes]
rs6576722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6576723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6670415	0.99[ASN][1000 genomes]
rs6670434	0.94[ASN][1000 genomes]
rs6682889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6687220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7524511	0.84[JPT][hapmap]
rs818525	0.83[ASN][1000 genomes]
rs9661716	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9662145	0.87[ASN][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	esv3349532	chr1:85154814-85157812	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2911571	LMO4	cis	parietal	SCAN
rs2911571	Y_RNA	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85153600-85157000	Active TSS	K562	blood
2	chr1:85153600-85157400	Active TSS	Stomach Smooth Muscle	stomach
3	chr1:85154400-85157000	Active TSS	H1 Cell Line	embryonic stem cell
4	chr1:85154400-85157200	Active TSS	A549	lung
5	chr1:85154600-85157000	Active TSS	Psoas Muscle	Psoas
6	chr1:85154600-85157400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:85154800-85157000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:85154800-85157000	Active TSS	Aorta	Aorta
9	chr1:85154800-85157200	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr1:85154800-85157600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:85155000-85157000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:85155000-85157000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:85155000-85157000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:85155000-85157000	Active TSS	Right Ventricle	heart
15	chr1:85155000-85157200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:85155000-85157400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr1:85155000-85157400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:85155200-85157000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:85155200-85157000	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr1:85155200-85157000	Active TSS	Fetal Stomach	stomach
21	chr1:85155200-85157000	Active TSS	Pancreas	Pancrea
22	chr1:85155200-85157000	Active TSS	Stomach Mucosa	stomach
23	chr1:85155200-85157000	Active TSS	NHDF-Ad	bronchial
24	chr1:85155200-85157200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr1:85155200-85157200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:85155200-85157200	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr1:85155400-85157000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:85155400-85157000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:85155400-85157000	Active TSS	Brain Angular Gyrus	brain
30	chr1:85155400-85157000	Active TSS	Esophagus	oesophagus
31	chr1:85155400-85157000	Active TSS	Fetal Kidney	kidney
32	chr1:85155400-85157000	Active TSS	Gastric	stomach
33	chr1:85155400-85157000	Active TSS	Ovary	ovary
34	chr1:85155400-85157000	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr1:85155400-85157000	Active TSS	Small Intestine	intestine
36	chr1:85155400-85157200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:85155400-85157200	Active TSS	Thymus	Thymus
38	chr1:85155400-85157400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:85155600-85157200	Active TSS	HepG2	liver
40	chr1:85156400-85157000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
41	chr1:85156400-85157000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr1:85156400-85157000	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:85156400-85157000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:85156400-85157000	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr1:85156400-85157000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr1:85156400-85157000	Active TSS	Fetal Heart	heart
47	chr1:85156400-85157000	Flanking Active TSS	Fetal Muscle Trunk	muscle
48	chr1:85156400-85157000	Flanking Active TSS	Placenta	Placenta
49	chr1:85156400-85157000	Active TSS	Right Atrium	heart
50	chr1:85156400-85157200	Flanking Active TSS	Primary B cells from cord blood	blood

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