Variant report

Variant	rs3087857
Chromosome Location	chr2:47146046-47146047
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	RAD21	chr2:47145925-47146387	A549	lung:	n/a	chr2:47146176-47146195
2	CTCF	chr2:47146040-47146190	HEK293	kidney:	n/a	n/a
3	RAD21	chr2:47145908-47146448	HepG2	liver:	n/a	chr2:47146176-47146195
4	RAD21	chr2:47146018-47146349	HepG2	liver:	n/a	chr2:47146176-47146195
5	RAD21	chr2:47146012-47146330	HepG2	liver:	n/a	chr2:47146176-47146195
6	CTCF	chr2:47146013-47146331	K562	blood:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
7	RAD21	chr2:47146030-47146391	SK-N-SH_RA	brain:	n/a	chr2:47146176-47146195
8	ZNF143	chr2:47145984-47146365	GM12878	blood:	n/a	n/a
9	CTCF	chr2:47146040-47146190	Hela-S3	cervix:	n/a	n/a
10	CTCF	chr2:47146029-47146305	SK-N-SH_RA	brain:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
11	RAD21	chr2:47145992-47146328	A549	lung:	n/a	chr2:47146176-47146195
12	RAD21	chr2:47145172-47146557	SK-N-SH	brain:	n/a	chr2:47146176-47146195
13	SMC3	chr2:47145976-47146317	HepG2	liver:	n/a	n/a
14	CBX3	chr2:47146045-47146356	K562	blood:	n/a	n/a
15	CTCF	chr2:47145957-47146366	IMR90	lung:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
16	CTCF	chr2:47145992-47146313	SK-N-SH_RA	brain:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
17	RAD21	chr2:47146002-47146365	GM12878	blood:	n/a	chr2:47146176-47146195
18	RFX5	chr2:47145999-47146321	Hela-S3	cervix:	n/a	n/a
19	RAD21	chr2:47146013-47146297	GM12878	blood:	n/a	chr2:47146176-47146195
20	RAD21	chr2:47145973-47146368	IMR90	lung:	n/a	chr2:47146176-47146195
21	CTCF	chr2:47145952-47146395	HepG2	liver:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
22	RAD21	chr2:47145951-47146348	ECC-1	luminal epithelium:	n/a	chr2:47146176-47146195
23	WRNIP1	chr2:47145866-47146193	GM12878	blood:	n/a	n/a
24	CTCF	chr2:47146045-47146295	MCF-7	breast:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
25	CTCF	chr2:47145487-47146566	A549	lung:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
26	ZNF143	chr2:47146004-47146333	K562	blood:	n/a	n/a
27	CTCF	chr2:47146027-47146312	GM12878	blood:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
28	CTCF	chr2:47145975-47146288	H1-hESC	embryonic stem cell:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
29	CTCF	chr2:47145877-47146430	HCT-116	colon:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
30	YY1	chr2:47146031-47146212	K562	blood:	n/a	n/a
31	RAD21	chr2:47145979-47146364	Hela-S3	cervix:	n/a	chr2:47146176-47146195
32	RAD21	chr2:47145988-47146323	H1-hESC	embryonic stem cell:	n/a	chr2:47146176-47146195
33	RAD21	chr2:47146040-47146287	K562	blood:	n/a	chr2:47146176-47146195
34	CTCF	chr2:47146040-47146190	GM12873	blood:	n/a	n/a
35	CTCF	chr2:47146013-47146259	HepG2	liver:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
36	MAZ	chr2:47146019-47146283	K562	blood:	n/a	n/a
37	RCOR1	chr2:47146039-47146276	K562	blood:	n/a	n/a
38	RAD21	chr2:47145811-47146558	HCT-116	colon:	n/a	chr2:47146176-47146195
39	RAD21	chr2:47145916-47146421	H1-hESC	embryonic stem cell:	n/a	chr2:47146176-47146195
40	CTCF	chr2:47146035-47146312	Spleen_OC	spleen:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
41	CTCF	chr2:47146040-47146190	HRE	kidney:	n/a	n/a
42	CTCF	chr2:47146041-47146299	K562	blood:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
43	RAD21	chr2:47146015-47146295	SK-N-SH_RA	brain:	n/a	chr2:47146176-47146195
44	CTCF	chr2:47145835-47146384	GM12878	blood:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
45	RAD21	chr2:47145950-47146330	MCF-7	breast:	n/a	chr2:47146176-47146195
46	RAD21	chr2:47145967-47146324	GM12878	blood:	n/a	chr2:47146176-47146195
47	YY1	chr2:47145979-47146253	GM12878	blood:	n/a	n/a
48	CTCF	chr2:47146040-47146190	HCT-116	colon:	n/a	n/a
49	CTCF	chr2:47145970-47146426	MCF-7	breast:	n/a	chr2:47146175-47146193 chr2:47146177-47146198 chr2:47146176-47146192
50	ZNF143	chr2:47146023-47146326	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:47146010-47146060	HMEC	breast:	n/a
2	chr2:47146010-47146060	HAEpiC	amniotic membrane:	n/a
3	chr2:47146010-47146060	AG09319	gingival:	n/a
4	chr2:47146010-47146060	SK-N-MC	brain:	n/a
5	chr2:47146010-47146060	Caco-2	colon:	n/a
6	chr2:47146010-47146060	HRE	kidney:	n/a
7	chr2:47146010-47146060	SKMC	muscle:	n/a
8	chr2:47146010-47146060	MCF10A-Er-Src	breast:	n/a
9	chr2:47146010-47146060	Jurkat	blood:	n/a
10	chr2:47146010-47146060	HCT-116	colon:	n/a
11	chr2:47146010-47146060	HepG2	liver:	n/a
12	chr2:47146010-47146060	PANC-1	pancreas:	n/a
13	chr2:47146010-47146060	U87	brain:	n/a
14	chr2:47146010-47146060	HPAEpiC	pulmonary alveolar:	n/a
15	chr2:47146010-47146060	PFSK-1	brain:	n/a
16	chr2:47146010-47146060	BJ	skin:	n/a
17	chr2:47146010-47146060	IMR90	lung:	fetal
18	chr2:47146010-47146060	NH-A	brain:	n/a
19	chr2:47146010-47146060	SK-N-SH	brain:	n/a
20	chr2:47146010-47146060	HL-60	blood:	n/a
21	chr2:47146010-47146060	ProgFib	skin:	n/a
22	chr2:47146010-47146060	HNPCEpiC	eye:	n/a
23	chr2:47146010-47146060	ECC-1	luminal epithelium:	n/a
24	chr2:47146010-47146060	GM12878	blood:	n/a
25	chr2:47146010-47146060	MCF-7	breast:	n/a
26	chr2:47146010-47146060	HCF	heart:	n/a
27	chr2:47146010-47146060	RPTEC	kidney:	n/a
28	chr2:47146010-47146060	NT2-D1	testis:	n/a
29	chr2:47146010-47146060	HRCEpiC	kidney:	n/a
30	chr2:47146010-47146060	Hela-S3	cervix:	n/a
31	chr2:47146010-47146060	HIPEpiC	eye:	n/a
32	chr2:47146010-47146060	T-47D	breast:	n/a
33	chr2:47146010-47146060	AoSMC	blood vessel:	n/a
34	chr2:47146010-47146060	GM06990	blood:	n/a
35	chr2:47146010-47146060	LNCaP	prostate:	n/a
36	chr2:47146010-47146060	HRPEpiC	eye:	n/a
37	chr2:47146010-47146060	NHBE	bronchial:	n/a
38	chr2:47146010-47146060	GM19239	blood:	n/a
39	chr2:47146010-47146060	H1-hESC	embryonic stem cell:	embryo
40	chr2:47146010-47146060	K562	blood:	n/a
41	chr2:47146010-47146060	HCM	heart:	n/a
42	chr2:47146010-47146060	ovcar-3	ovarian:	n/a
43	chr2:47146010-47146060	HCPEpiC	choroid plexus:	n/a
44	chr2:47146010-47146060	Hepatocyte	liver:	n/a
45	chr2:47146010-47146060	AG10803	skin:	n/a
46	chr2:47146010-47146060	BE2_C	brain:	n/a
47	chr2:47146010-47146060	NHDF-neo	bronchial:	n/a
48	chr2:47146010-47146060	PrEC	prostate:	n/a
49	chr2:47146010-47146060	GM12892	blood:	n/a
50	chr2:47146010-47146060	CMK	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:47145255..47147590-chr2:47169697..47171236,2	K562	blood:
2	chr2:47142780..47146808-chr2:47401206..47405117,7	K562	blood:
3	chr2:47144874..47146939-chr2:47165957..47169757,3	K562	blood:
4	chr2:47145752..47146265-chr2:47550305..47551182,2	MCF-7	breast:
5	chr2:47145665..47146215-chr2:47550065..47550907,2	K562	blood:
6	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
7	chr2:47144648..47146323-chr2:47215712..47217737,2	MCF-7	breast:
8	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
9	chr2:47145956..47148459-chr2:47233985..47235692,2	K562	blood:
10	chr2:47143277..47146895-chr2:47166934..47170660,7	MCF-7	breast:
11	chr2:47145823..47146685-chr2:47549951..47550860,4	MCF-7	breast:

Variant related genes	Relation type
MCFD2	TF binding region
MCFD2	CpG island
ENSG00000180398	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10174894	0.96[ASN][1000 genomes]
rs10199965	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10495940	0.88[CEU][hapmap]
rs11890177	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.94[ASN][1000 genomes]
rs11894319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13388612	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13392448	0.94[ASN][1000 genomes]
rs13398851	0.87[ASN][1000 genomes]
rs1446499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1446500	1.00[ASN][1000 genomes]
rs17035859	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs17035867	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs17035884	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17035887	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17036060	0.88[CHB][hapmap]
rs2084192	1.00[ASN][1000 genomes]
rs2289927	0.96[ASN][1000 genomes]
rs2289928	0.96[ASN][1000 genomes]
rs2347259	0.88[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs28516550	0.94[ASN][1000 genomes]
rs34581142	0.96[ASN][1000 genomes]
rs35433380	0.96[ASN][1000 genomes]
rs4505575	0.81[ASN][1000 genomes]
rs55872217	0.96[ASN][1000 genomes]
rs56213467	0.96[ASN][1000 genomes]
rs58589709	0.94[ASN][1000 genomes]
rs60194846	1.00[ASN][1000 genomes]
rs61132855	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62136818	0.85[ASN][1000 genomes]
rs62136819	0.85[ASN][1000 genomes]
rs62136820	0.88[ASN][1000 genomes]
rs62136822	0.94[ASN][1000 genomes]
rs62136823	0.96[ASN][1000 genomes]
rs62136825	0.96[ASN][1000 genomes]
rs62136827	0.96[ASN][1000 genomes]
rs62140550	1.00[ASN][1000 genomes]
rs62140553	0.84[ASN][1000 genomes]
rs6544938	0.98[ASN][1000 genomes]
rs6544939	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs6706031	0.96[ASN][1000 genomes]
rs6715391	0.94[ASN][1000 genomes]
rs6715620	1.00[ASN][1000 genomes]
rs6716381	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6722440	0.96[ASN][1000 genomes]
rs6729120	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6729604	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6733548	1.00[ASN][1000 genomes]
rs6743966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6743994	0.94[ASN][1000 genomes]
rs6745578	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6755303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6758093	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs6758512	0.96[ASN][1000 genomes]
rs6759170	0.88[CEU][hapmap]
rs71423929	1.00[ASN][1000 genomes]
rs7340475	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs73926966	1.00[ASN][1000 genomes]
rs754411	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs7565420	0.90[ASN][1000 genomes]
rs7574514	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs7574833	0.84[ASW][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs7575172	1.00[ASN][1000 genomes]
rs7586004	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7596198	0.94[ASN][1000 genomes]
rs7601491	0.80[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs8861	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9973504	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3087857	MCFD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47143800-47146200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:47143800-47146200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
3	chr2:47143800-47146200	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr2:47143800-47146400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr2:47143800-47147200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:47143800-47147200	Enhancers	Primary B cells from peripheral blood	blood
7	chr2:47143800-47148800	Weak transcription	NH-A	brain
8	chr2:47143800-47149000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:47143800-47151800	Weak transcription	Lung	lung
10	chr2:47144000-47146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr2:47144000-47146200	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:47144000-47146200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr2:47144000-47148800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:47144000-47150800	Weak transcription	Placenta	Placenta
15	chr2:47144200-47146200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:47144200-47146600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:47144200-47148400	Weak transcription	HUVEC	blood vessel
18	chr2:47144200-47149200	Weak transcription	NHDF-Ad	bronchial
19	chr2:47144200-47149800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:47144200-47150000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:47144200-47150200	Weak transcription	Gastric	stomach
22	chr2:47144200-47151800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr2:47144200-47153000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:47144200-47153200	Weak transcription	Fetal Stomach	stomach
25	chr2:47144200-47153800	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr2:47144200-47154000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr2:47144200-47155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:47144200-47157200	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:47144200-47166600	Weak transcription	Pancreas	Pancrea
30	chr2:47144400-47146800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr2:47144400-47146800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:47144400-47147000	Enhancers	Primary B cells from cord blood	blood
33	chr2:47144400-47147200	Enhancers	Primary T cells from cord blood	blood
34	chr2:47144400-47149000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:47144400-47153000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr2:47144400-47153000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:47144400-47154400	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:47144600-47146200	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr2:47144600-47146800	Weak transcription	Psoas Muscle	Psoas
40	chr2:47144600-47149000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:47144600-47149800	Weak transcription	Fetal Intestine Large	intestine
42	chr2:47144600-47149800	Weak transcription	Fetal Intestine Small	intestine
43	chr2:47144600-47149800	Weak transcription	HMEC	breast
44	chr2:47144600-47153000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:47144600-47153000	Weak transcription	Brain Germinal Matrix	brain
46	chr2:47144600-47164600	Weak transcription	Spleen	Spleen
47	chr2:47144800-47146200	Enhancers	HepG2	liver
48	chr2:47144800-47146800	Enhancers	Fetal Thymus	thymus
49	chr2:47144800-47149000	Weak transcription	NHEK	skin
50	chr2:47144800-47149800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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