Variant report

Variant	rs2291721
Chromosome Location	chr3:47205905-47205906
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	YY1	chr3:47205382-47206157	ECC-1	luminal epithelium:	n/a	chr3:47205587-47205598 chr3:47205468-47205479
2	POLR2A	chr3:47205065-47206407	GM18951	blood:	n/a	n/a
3	PBX3	chr3:47205540-47206120	A549	lung:	n/a	n/a
4	YY1	chr3:47204498-47206409	GM12878	blood:	n/a	chr3:47205587-47205598 chr3:47205468-47205479 chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
5	SIN3A	chr3:47205444-47206483	GM12878	blood:	n/a	chr3:47205749-47205760 chr3:47206305-47206316 chr3:47205587-47205598
6	MAZ	chr3:47204647-47206459	Hela-S3	cervix:	n/a	chr3:47205889-47205899
7	BCLAF1	chr3:47205517-47205927	GM12878	blood:	n/a	chr3:47205768-47205781 chr3:47205884-47205897
8	PAX5	chr3:47204710-47206375	GM12892	blood:	n/a	n/a
9	NFIC	chr3:47205569-47206474	GM12878	blood:	n/a	n/a
10	BACH1	chr3:47205775-47206184	H1-hESC	embryonic stem cell:	n/a	n/a
11	EP300	chr3:47205525-47205980	HepG2	liver:	n/a	n/a
12	MAX	chr3:47204474-47206415	K562	blood:	n/a	chr3:47205889-47205899
13	SIN3AK20	chr3:47204525-47206286	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr3:47205295-47206182	A549	lung:	n/a	n/a
15	POLR2A	chr3:47204597-47206503	H1-neurons	neurons:	n/a	n/a
16	RCOR1	chr3:47205656-47206526	K562	blood:	n/a	n/a
17	TEAD4	chr3:47204732-47206081	SK-N-SH	brain:	n/a	n/a
18	TBL1XR1	chr3:47205385-47206677	K562	blood:	n/a	n/a
19	YY1	chr3:47205521-47206430	GM12891	blood:	n/a	chr3:47205587-47205598
20	POLR2A	chr3:47204777-47206501	K562	blood:	n/a	n/a
21	SMC3	chr3:47205592-47206646	GM12878	blood:	n/a	n/a
22	MYC	chr3:47204469-47206552	K562	blood:	n/a	chr3:47205889-47205899
23	TRIM28	chr3:47205411-47206167	K562	blood:	n/a	n/a
24	HEY1	chr3:47204946-47206400	K562	blood:	n/a	chr3:47205280-47205295 chr3:47206302-47206317 chr3:47205318-47205333
25	MYC	chr3:47204783-47206024	MCF-7	breast:	n/a	chr3:47205889-47205899
26	POLR2A	chr3:47205478-47205906	U87	brain:	n/a	n/a
27	MAX	chr3:47204399-47206611	HCT-116	colon:	n/a	chr3:47205889-47205899
28	REST	chr3:47204200-47206694	H1-neurons	neurons:	n/a	chr3:47205082-47205095
29	CTCF	chr3:47205780-47205930	GM12874	blood:	n/a	chr3:47205889-47205902
30	NFIC	chr3:47205287-47205982	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr3:47204689-47206436	Hela-S3	cervix:	n/a	n/a
32	RELA	chr3:47205482-47206701	GM15510	blood:	n/a	n/a
33	POLR2A	chr3:47205345-47206058	A549	lung:	n/a	n/a
34	CREB1	chr3:47205343-47206426	GM12878	blood:	n/a	n/a
35	YY1	chr3:47204531-47206395	K562	blood:	n/a	chr3:47205587-47205598 chr3:47205468-47205479 chr3:47205189-47205198 chr3:47205321-47205332 chr3:47205279-47205293 chr3:47205256-47205270 chr3:47204848-47204862 chr3:47205252-47205266 chr3:47205258-47205267 chr3:47205253-47205267 chr3:47205109-47205118
36	CHD1	chr3:47204412-47206570	H1-hESC	embryonic stem cell:	n/a	chr3:47205244-47205254
37	POLR2A	chr3:47204969-47206455	H1-hESC	embryonic stem cell:	n/a	n/a
38	CTCF	chr3:47205860-47206010	GM12878	blood:	n/a	chr3:47205889-47205902
39	CTCF	chr3:47205840-47205990	GM12872	blood:	n/a	chr3:47205889-47205902
40	ARID3A	chr3:47205658-47205920	HepG2	liver:	n/a	n/a
41	SIN3AK20	chr3:47205594-47205990	PFSK-1	brain:	n/a	n/a
42	CTCF	chr3:47205880-47206030	WERI-Rb-1	eye:	n/a	chr3:47205889-47205902
43	POLR2A	chr3:47205242-47206497	SK-N-SH	brain:	n/a	n/a
44	CTCF	chr3:47205860-47206010	GM12873	blood:	n/a	chr3:47205889-47205902
45	TBP	chr3:47205565-47206578	GM12878	blood:	n/a	n/a
46	POLR2A	chr3:47204896-47206417	PBDE	blood:	n/a	n/a
47	POLR2A	chr3:47205116-47206340	Gliobla	brain:	n/a	n/a
48	POLR2A	chr3:47205235-47206316	Hela-S3	cervix:	n/a	n/a
49	USF2	chr3:47205730-47205930	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr3:47205604-47205939	K562	blood:	n/a	chr3:47205889-47205902

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:47205858-47205908	SKMC	muscle:	n/a
2	chr3:47205858-47205908	HMEC	breast:	n/a
3	chr3:47205858-47205908	T-47D	breast:	n/a
4	chr3:47205858-47205908	HAEpiC	amniotic membrane:	n/a
5	chr3:47205858-47205908	CMK	blood:	n/a
6	chr3:47205858-47205908	SAEC	small airway:	n/a
7	chr3:47205858-47205908	Hepatocyte	liver:	n/a
8	chr3:47205858-47205908	BE2_C	brain:	n/a
9	chr3:47205858-47205908	Jurkat	blood:	n/a
10	chr3:47205858-47205908	SK-N-MC	brain:	n/a
11	chr3:47205858-47205908	NB4	blood:	n/a
12	chr3:47205858-47205908	HRPEpiC	eye:	n/a
13	chr3:47205858-47205908	Hela-S3	cervix:	n/a
14	chr3:47205858-47205908	AoSMC	blood vessel:	n/a
15	chr3:47205858-47205908	HL-60	blood:	n/a
16	chr3:47205858-47205908	LNCaP	prostate:	n/a
17	chr3:47205858-47205908	MCF-7	breast:	n/a
18	chr3:47205858-47205908	U87	brain:	n/a
19	chr3:47205858-47205908	K562	blood:	n/a
20	chr3:47205858-47205908	HRCEpiC	kidney:	n/a
21	chr3:47205858-47205908	AG09319	gingival:	n/a
22	chr3:47205858-47205908	ProgFib	skin:	n/a
23	chr3:47205858-47205908	PFSK-1	brain:	n/a
24	chr3:47205858-47205908	PrEC	prostate:	n/a
25	chr3:47205858-47205908	H1-hESC	embryonic stem cell:	embryo
26	chr3:47205858-47205908	SK-N-SH	brain:	n/a
27	chr3:47205858-47205908	NHDF-neo	bronchial:	n/a
28	chr3:47205858-47205908	A549	lung:	n/a
29	chr3:47205858-47205908	HepG2	liver:	n/a
30	chr3:47205858-47205908	HNPCEpiC	eye:	n/a
31	chr3:47205858-47205908	ovcar-3	ovarian:	n/a
32	chr3:47205858-47205908	ECC-1	luminal epithelium:	n/a
33	chr3:47205858-47205908	PANC-1	pancreas:	n/a
34	chr3:47205858-47205908	HCT-116	colon:	n/a
35	chr3:47205858-47205908	GM12892	blood:	n/a
36	chr3:47205858-47205908	HEK293	kidney:	embryo
37	chr3:47205858-47205908	HIPEpiC	eye:	n/a
38	chr3:47205858-47205908	GM12891	blood:	n/a
39	chr3:47205858-47205908	HCM	heart:	n/a
40	chr3:47205858-47205908	HCF	heart:	n/a
41	chr3:47205858-47205908	HEEpiC	esophagus:	n/a
42	chr3:47205858-47205908	RPTEC	kidney:	n/a
43	chr3:47205858-47205908	NH-A	brain:	n/a
44	chr3:47205858-47205908	IMR90	lung:	fetal
45	chr3:47205858-47205908	GM19239	blood:	n/a
46	chr3:47205858-47205908	SK-N-SH_RA	brain:	n/a
47	chr3:47205858-47205908	AG09309	skin:	n/a
48	chr3:47205858-47205908	AG10803	skin:	n/a
49	chr3:47205858-47205908	BJ	skin:	n/a
50	chr3:47205858-47205908	MCF10A-Er-Src	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:47047075..47049174-chr3:47204688..47207568,2	K562	blood:
2	chr3:47204122..47207133-chr3:47321636..47325818,4	K562	blood:
3	chr3:47204211..47206785-chr3:47421682..47423744,2	K562	blood:
4	chr3:47204839..47206673-chr3:47316671..47318992,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL18-1	chr3:47205720-47206087	XLOC_002636
2	lnc-KLHL18-1	chr3:47205469-47206087	NONHSAT089476
3	lnc-KLHL18-1	chr3:47205860-47206087	NONHSAT089478
4	lnc-KLHL18-1	chr3:47205721-47206087	XLOC_002636

Variant related genes	Relation type
KIF9-AS1	TF binding region
SETD2	TF binding region
SETD2	CpG island
KIF9-AS1	CpG island
ENSG00000260236	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000160796	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000114648	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12487863	0.89[AMR][1000 genomes]
rs12490244	0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12490251	0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12492463	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12493723	0.95[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12495173	0.84[AMR][1000 genomes]
rs12495438	0.82[ASN][1000 genomes]
rs3733093	0.84[AMR][1000 genomes]
rs3933020	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4082156	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4627772	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4683318	0.92[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4683321	0.87[AMR][1000 genomes]
rs4683323	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs58206566	0.82[ASN][1000 genomes]
rs59601660	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7638049	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1007714	chr3:47084387-47331570	Transcr. at gene 5' and 3' Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv590210	chr3:47126543-47214122	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv590211	chr3:47189485-47256057	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv3801	chr3:47201530-47246438	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr3:47203000-47207600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:47203200-47207400	Active TSS	GM12878-XiMat	blood
3	chr3:47203200-47207600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr3:47203400-47207200	Active TSS	Ovary	ovary
5	chr3:47203600-47206600	Active TSS	Right Ventricle	heart
6	chr3:47203600-47207200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:47203600-47207200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr3:47203600-47207200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:47203600-47207200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:47203600-47207200	Active TSS	HSMMtube	muscle
11	chr3:47203800-47206000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:47203800-47206600	Active TSS	Brain Germinal Matrix	brain
13	chr3:47203800-47206600	Active TSS	Fetal Thymus	thymus
14	chr3:47203800-47207000	Active TSS	Psoas Muscle	Psoas
15	chr3:47203800-47207200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:47203800-47207200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:47203800-47207200	Active TSS	Fetal Intestine Large	intestine
18	chr3:47203800-47207200	Active TSS	Fetal Intestine Small	intestine
19	chr3:47203800-47207200	Active TSS	Stomach Smooth Muscle	stomach
20	chr3:47203800-47207600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:47203800-47207600	Active TSS	H1 Cell Line	embryonic stem cell
22	chr3:47203800-47207600	Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr3:47204000-47206600	Active TSS	Sigmoid Colon	Sigmoid Colon
24	chr3:47204000-47206800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr3:47204000-47206800	Active TSS	Fetal Muscle Leg	muscle
26	chr3:47204000-47206800	Active TSS	Stomach Mucosa	stomach
27	chr3:47204000-47207000	Active TSS	H9 Cell Line	embryonic stem cell
28	chr3:47204000-47207000	Active TSS	Aorta	Aorta
29	chr3:47204000-47207000	Active TSS	Fetal Stomach	stomach
30	chr3:47204000-47207200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:47204000-47207400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:47204000-47207400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr3:47204000-47207400	Active TSS	NHDF-Ad	bronchial
34	chr3:47204200-47206400	Active TSS	Small Intestine	intestine
35	chr3:47204200-47206800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr3:47204200-47206800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:47204200-47206800	Active TSS	Fetal Muscle Trunk	muscle
38	chr3:47204200-47206800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr3:47204200-47207000	Active TSS	Colonic Mucosa	Colon
40	chr3:47204200-47207000	Active TSS	Esophagus	oesophagus
41	chr3:47204200-47207000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr3:47204200-47207000	Active TSS	Placenta	Placenta
43	chr3:47204200-47207000	Active TSS	Gastric	stomach
44	chr3:47204200-47207000	Active TSS	Lung	lung
45	chr3:47204200-47207000	Active TSS	Pancreas	Pancrea
46	chr3:47204200-47207000	Active TSS	NH-A	brain
47	chr3:47204200-47207000	Active TSS	NHEK	skin
48	chr3:47204200-47207200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr3:47204200-47207200	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:47204200-47207200	Active TSS	Left Ventricle	heart

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