Variant report

Variant	rs3811520
Chromosome Location	chr2:48667764-48667765
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	CTCF	chr2:48667700-48667850	NHLF	lung:	n/a	chr2:48667775-48667785 chr2:48667774-48667787
2	EGR1	chr2:48667266-48668303	HCT-116	colon:	n/a	chr2:48668078-48668091 chr2:48667890-48667903 chr2:48667931-48667940 chr2:48668028-48668041 chr2:48667887-48667901 chr2:48668180-48668190 chr2:48667819-48667828
3	TAL1	chr2:48667487-48667831	K562	blood:	n/a	n/a
4	TBP	chr2:48667509-48667994	HepG2	liver:	n/a	n/a
5	YY1	chr2:48667171-48668120	SK-N-SH_RA	brain:	n/a	chr2:48667745-48667767 chr2:48667767-48667775 chr2:48667762-48667779 chr2:48668078-48668089 chr2:48667756-48667778 chr2:48667761-48667780 chr2:48667887-48667901 chr2:48667748-48667756 chr2:48668053-48668067 chr2:48667743-48667760 chr2:48667745-48667755
6	E2F6	chr2:48667309-48668212	A549	lung:	n/a	chr2:48668034-48668049 chr2:48667768-48667782 chr2:48668033-48668045
7	CTCF	chr2:48667720-48667870	AG04449	skin:	n/a	chr2:48667775-48667785 chr2:48667774-48667787
8	POLR2A	chr2:48667295-48668807	GM12892	blood:	n/a	n/a
9	RCOR1	chr2:48667262-48667800	K562	blood:	n/a	n/a
10	SIN3AK20	chr2:48667215-48667777	H1-hESC	embryonic stem cell:	n/a	n/a
11	MXI1	chr2:48667290-48668431	HepG2	liver:	n/a	chr2:48667567-48667582 chr2:48668199-48668214 chr2:48667569-48667584
12	TAF1	chr2:48667526-48667938	GM12892	blood:	n/a	n/a
13	RFX5	chr2:48667356-48667884	GM12878	blood:	n/a	chr2:48667568-48667583 chr2:48667569-48667578 chr2:48667568-48667583 chr2:48667566-48667580 chr2:48667567-48667584 chr2:48667568-48667583
14	MAX	chr2:48667394-48668154	K562	blood:	n/a	chr2:48667573-48667582 chr2:48667569-48667578 chr2:48667870-48667880
15	CTCF	chr2:48667720-48667870	HCPEpiC	choroid plexus:	n/a	chr2:48667775-48667785 chr2:48667774-48667787
16	TEAD4	chr2:48667335-48668003	K562	blood:	n/a	n/a
17	JUND	chr2:48667434-48668461	A549	lung:	n/a	chr2:48667757-48667768
18	CREB1	chr2:48667558-48668201	K562	blood:	n/a	n/a
19	HEY1	chr2:48667418-48668323	HepG2	liver:	n/a	chr2:48667888-48667903
20	BCLAF1	chr2:48667199-48668375	GM12878	blood:	n/a	chr2:48667888-48667897 chr2:48668078-48668087 chr2:48667931-48667940 chr2:48668185-48668198
21	HEY1	chr2:48667393-48668175	K562	blood:	n/a	chr2:48667888-48667903
22	YY1	chr2:48667389-48667974	NT2-D1	testis:	n/a	chr2:48667745-48667767 chr2:48667767-48667775 chr2:48667762-48667779 chr2:48667756-48667778 chr2:48667761-48667780 chr2:48667887-48667901 chr2:48667748-48667756 chr2:48667743-48667760 chr2:48667745-48667755
23	FOXA2	chr2:48667559-48668002	A549	lung:	n/a	n/a
24	POLR2A	chr2:48667410-48668475	GM18951	blood:	n/a	n/a
25	CTCF	chr2:48667700-48667850	HepG2	liver:	n/a	chr2:48667775-48667785 chr2:48667774-48667787
26	CTCF	chr2:48667640-48667790	HRE	kidney:	n/a	chr2:48667775-48667785 chr2:48667774-48667787
27	POLR2A	chr2:48667472-48668227	K562	blood:	n/a	n/a
28	SIN3AK20	chr2:48667211-48668590	SK-N-SH	brain:	n/a	n/a
29	GABPA	chr2:48667171-48668090	A549	lung:	n/a	n/a
30	CHD2	chr2:48667553-48667884	K562	blood:	n/a	n/a
31	POLR2A	chr2:48667212-48668730	HepG2	liver:	n/a	n/a
32	CHD2	chr2:48667477-48668518	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr2:48667660-48667810	BJ	skin:	n/a	chr2:48667775-48667785 chr2:48667774-48667787
34	MTA3	chr2:48667199-48668636	GM12878	blood:	n/a	n/a
35	ZNF384	chr2:48667311-48667915	GM12878	blood:	n/a	n/a
36	POLR2A	chr2:48667447-48668382	A549	lung:	n/a	n/a
37	CREB1	chr2:48667530-48667967	A549	lung:	n/a	n/a
38	CTCF	chr2:48667700-48667850	HMF	breast:	n/a	chr2:48667775-48667785 chr2:48667774-48667787
39	YY1	chr2:48667299-48668443	GM12892	blood:	n/a	chr2:48667745-48667767 chr2:48667767-48667775 chr2:48667762-48667779 chr2:48668078-48668089 chr2:48667756-48667778 chr2:48667761-48667780 chr2:48667887-48667901 chr2:48667748-48667756 chr2:48668053-48668067 chr2:48667743-48667760 chr2:48667745-48667755
40	SIN3AK20	chr2:48667200-48668419	PANC-1	pancreas:	n/a	n/a
41	E2F4	chr2:48667285-48668070	K562	blood:	n/a	chr2:48667835-48667846 chr2:48668034-48668049 chr2:48667768-48667782 chr2:48668033-48668045
42	YY1	chr2:48667310-48668423	K562	blood:	n/a	chr2:48667745-48667767 chr2:48667767-48667775 chr2:48667762-48667779 chr2:48668078-48668089 chr2:48667756-48667778 chr2:48667761-48667780 chr2:48667887-48667901 chr2:48667748-48667756 chr2:48668053-48668067 chr2:48667743-48667760 chr2:48667745-48667755
43	MAZ	chr2:48667410-48668488	K562	blood:	n/a	chr2:48667573-48667582 chr2:48668179-48668189 chr2:48667569-48667578 chr2:48667870-48667880
44	ELK1	chr2:48667577-48667864	K562	blood:	n/a	n/a
45	YY1	chr2:48667318-48668469	K562	blood:	n/a	chr2:48667745-48667767 chr2:48667767-48667775 chr2:48667762-48667779 chr2:48668078-48668089 chr2:48667756-48667778 chr2:48667761-48667780 chr2:48667887-48667901 chr2:48667748-48667756 chr2:48668053-48668067 chr2:48667743-48667760 chr2:48667745-48667755
46	POLR2A	chr2:48667162-48668482	HUVEC	blood vessel:	n/a	n/a
47	ZMIZ1	chr2:48667277-48668237	K562	blood:	n/a	n/a
48	PML	chr2:48667384-48667979	K562	blood:	n/a	n/a
49	REST	chr2:48667363-48668077	SK-N-SH	brain:	n/a	chr2:48667667-48667680
50	NANOG	chr2:48667518-48667887	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:48667747-48667797	GM12891	blood:	n/a
2	chr2:48667747-48667797	HEK293	kidney:	embryo
3	chr2:48667747-48667797	HUVEC	blood vessel:	n/a
4	chr2:48667747-48667797	AG09319	gingival:	n/a
5	chr2:48667747-48667797	GM06990	blood:	n/a
6	chr2:48667747-48667797	HMEC	breast:	n/a
7	chr2:48667747-48667797	GM12892	blood:	n/a
8	chr2:48667747-48667797	GM12878	blood:	n/a
9	chr2:48667747-48667797	PrEC	prostate:	n/a
10	chr2:48667747-48667797	T-47D	breast:	n/a
11	chr2:48667747-48667797	SK-N-SH	brain:	n/a
12	chr2:48667747-48667797	AG09309	skin:	n/a
13	chr2:48667747-48667797	HCT-116	colon:	n/a
14	chr2:48667747-48667797	Hela-S3	cervix:	n/a
15	chr2:48667747-48667797	PFSK-1	brain:	n/a
16	chr2:48667747-48667797	H1-hESC	embryonic stem cell:	embryo
17	chr2:48667747-48667797	NH-A	brain:	n/a
18	chr2:48667747-48667797	K562	blood:	n/a
19	chr2:48667747-48667797	Hepatocyte	liver:	n/a
20	chr2:48667747-48667797	Jurkat	blood:	n/a
21	chr2:48667747-48667797	LNCaP	prostate:	n/a
22	chr2:48667747-48667797	HAEpiC	amniotic membrane:	n/a
23	chr2:48667747-48667797	MCF-7	breast:	n/a
24	chr2:48667747-48667797	A549	lung:	n/a
25	chr2:48667747-48667797	HNPCEpiC	eye:	n/a
26	chr2:48667747-48667797	Caco-2	colon:	n/a
27	chr2:48667747-48667797	NT2-D1	testis:	n/a
28	chr2:48667747-48667797	U87	brain:	n/a
29	chr2:48667747-48667797	SK-N-MC	brain:	n/a
30	chr2:48667747-48667797	BE2_C	brain:	n/a
31	chr2:48667747-48667797	HCF	heart:	n/a
32	chr2:48667747-48667797	PANC-1	pancreas:	n/a
33	chr2:48667747-48667797	AG10803	skin:	n/a
34	chr2:48667747-48667797	HRE	kidney:	n/a
35	chr2:48667747-48667797	CMK	blood:	n/a
36	chr2:48667747-48667797	BJ	skin:	n/a
37	chr2:48667747-48667797	HPAEpiC	pulmonary alveolar:	n/a
38	chr2:48667747-48667797	IMR90	lung:	fetal
39	chr2:48667747-48667797	HRPEpiC	eye:	n/a
40	chr2:48667747-48667797	ProgFib	skin:	n/a
41	chr2:48667747-48667797	GM19239	blood:	n/a
42	chr2:48667747-48667797	HIPEpiC	eye:	n/a
43	chr2:48667747-48667797	HRCEpiC	kidney:	n/a
44	chr2:48667747-48667797	AG04449	skin:	fetal
45	chr2:48667747-48667797	MCF10A-Er-Src	breast:	n/a
46	chr2:48667747-48667797	RPTEC	kidney:	n/a
47	chr2:48667747-48667797	NHDF-neo	bronchial:	n/a
48	chr2:48667747-48667797	SAEC	small airway:	n/a
49	chr2:48667747-48667797	HCM	heart:	n/a
50	chr2:48667747-48667797	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:48666828..48669731-chr2:48691807..48694698,2	MCF-7	breast:
2	chr2:48009081..48011260-chr2:48666512..48669305,2	K562	blood:
3	chr17:62500259..62503119-chr2:48667200..48670117,2	MCF-7	breast:
4	chr2:48009330..48011315-chr2:48667151..48669363,2	MCF-7	breast:
5	chr2:48132531..48135272-chr2:48667743..48670607,2	K562	blood:
6	chr2:48540677..48543829-chr2:48665802..48669252,3	K562	blood:
7	chr1:153962792..153963676-chr2:48667297..48668086,2	Hela-S3	cervix:
8	chr2:48131056..48133889-chr2:48666649..48669305,2	MCF-7	breast:
9	chr2:48539557..48542081-chr2:48666297..48668955,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LHCGR-2	chr2:48667224-48667870	NONHSAT070622

Variant related genes	Relation type
PPP1R21	TF binding region
ENSG00000272663	TF binding region
PPP1R21	CpG island
ENSG00000272663	CpG island
ENSG00000116062	Chromatin interaction
ENSG00000162869	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000170802	Chromatin interaction
ENSG00000233230	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000138081	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10185212	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10865229	0.86[ASN][1000 genomes]
rs11677398	1.00[CEU][hapmap]
rs12477901	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs13386132	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap]
rs4328683	1.00[CEU][hapmap]
rs4371401	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4429520	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs4430989	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4464333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4952913	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs4953574	0.97[ASN][1000 genomes]
rs4953584	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4953588	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6545040	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6545043	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs6545044	1.00[CEU][hapmap]
rs6715766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6756820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes]
rs7355307	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7577850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7608588	1.00[CEU][hapmap];1.00[YRI][hapmap]

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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48666600-48668400	Active TSS	Fetal Brain Female	brain
2	chr2:48666600-48668600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:48666600-48668800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:48666800-48668200	Active TSS	Fetal Brain Male	brain
5	chr2:48666800-48668600	Active TSS	Fetal Kidney	kidney
6	chr2:48666800-48668600	Active TSS	A549	lung
7	chr2:48666800-48668800	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:48666800-48668800	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr2:48666800-48669000	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr2:48666800-48669000	Active TSS	GM12878-XiMat	blood
11	chr2:48667000-48668200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:48667000-48668200	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr2:48667000-48668400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr2:48667000-48668400	Active TSS	Brain Cingulate Gyrus	brain
15	chr2:48667000-48668400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr2:48667000-48668400	Active TSS	K562	blood
17	chr2:48667000-48668600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:48667000-48668600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:48667000-48668600	Active TSS	Fetal Intestine Large	intestine
20	chr2:48667000-48668600	Active TSS	HMEC	breast
21	chr2:48667000-48668600	Active TSS	HSMMtube	muscle
22	chr2:48667000-48668800	Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:48667000-48668800	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr2:48667000-48668800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:48667000-48668800	Bivalent/Poised TSS	HepG2	liver
26	chr2:48667000-48669000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:48667000-48669000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:48667000-48669000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:48667000-48669000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:48667000-48669000	Active TSS	Fetal Stomach	stomach
31	chr2:48667000-48669200	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr2:48667000-48669200	Active TSS	Brain Anterior Caudate	brain
33	chr2:48667000-48669200	Active TSS	Stomach Smooth Muscle	stomach
34	chr2:48667000-48669400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:48667000-48669400	Active TSS	NHDF-Ad	bronchial
36	chr2:48667000-48669400	Active TSS	NHLF	lung
37	chr2:48667200-48668200	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr2:48667200-48668400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr2:48667200-48668400	Active TSS	Muscle Satellite Cultured Cells	--
40	chr2:48667200-48668400	Active TSS	Fetal Lung	lung
41	chr2:48667200-48668400	Active TSS	Fetal Muscle Leg	muscle
42	chr2:48667200-48668400	Active TSS	Placenta	Placenta
43	chr2:48667200-48668400	Active TSS	Thymus	Thymus
44	chr2:48667200-48668600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:48667200-48668600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:48667200-48668600	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr2:48667200-48668600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr2:48667200-48668600	Active TSS	Colonic Mucosa	Colon
49	chr2:48667200-48668600	Active TSS	Colon Smooth Muscle	Colon
50	chr2:48667200-48668600	Active TSS	Esophagus	oesophagus

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