Variant report

Variant	rs67171462
Chromosome Location	chr2:209130767-209130768
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:604)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:604 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr2:209130611-209130906	HepG2	liver:	n/a	n/a
2	MBD4	chr2:209129927-209131651	HepG2	liver:	n/a	n/a
3	CREB1	chr2:209130155-209131109	ECC-1	luminal epithelium:	n/a	n/a
4	JUND	chr2:209130318-209130961	HepG2	liver:	n/a	n/a
5	CEBPB	chr2:209130216-209131085	HepG2	liver:	n/a	n/a
6	USF1	chr2:209130076-209131203	ECC-1	luminal epithelium:	n/a	n/a
7	ATF2	chr2:209130444-209130998	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr2:209130579-209131113	GM12891	blood:	n/a	n/a
9	TAF1	chr2:209130526-209131370	HepG2	liver:	n/a	n/a
10	TBL1XR1	chr2:209129765-209131669	GM12878	blood:	n/a	n/a
11	YY1	chr2:209130504-209131328	GM12878	blood:	n/a	chr2:209131242-209131256
12	ZBTB7A	chr2:209130620-209131215	K562	blood:	n/a	n/a
13	POLR2A	chr2:209130611-209131413	Hela-S3	cervix:	n/a	n/a
14	JUND	chr2:209130487-209131093	A549	lung:	n/a	n/a
15	GTF2B	chr2:209130472-209131119	K562	blood:	n/a	n/a
16	POLR2A	chr2:209130039-209131427	K562	blood:	n/a	n/a
17	ZBTB7A	chr2:209130592-209131259	HepG2	liver:	n/a	n/a
18	GTF2F1	chr2:209130635-209131067	K562	blood:	n/a	n/a
19	USF1	chr2:209130526-209131082	SK-N-SH_RA	brain:	n/a	n/a
20	MAX	chr2:209130016-209131566	ECC-1	luminal epithelium:	n/a	chr2:209130353-209130362
21	MYC	chr2:209129863-209131263	K562	blood:	n/a	chr2:209130353-209130362
22	CTCF	chr2:209130760-209130910	HFF	foreskin:	n/a	n/a
23	SPI1	chr2:209130737-209131187	GM12891	blood:	n/a	chr2:209130966-209130979
24	EGR1	chr2:209130646-209131136	GM12878	blood:	n/a	n/a
25	GATA1	chr2:209129668-209131288	K562	blood:	n/a	chr2:209130018-209130025 chr2:209130324-209130332
26	POLR2A	chr2:209129927-209131567	GM12892	blood:	n/a	n/a
27	YY1	chr2:209130567-209131064	HCT-116	colon:	n/a	n/a
28	HNF4G	chr2:209130465-209131062	HepG2	liver:	n/a	chr2:209130751-209130758 chr2:209130747-209130763
29	ATF3	chr2:209130496-209131098	A549	lung:	n/a	n/a
30	POLR2A	chr2:209129919-209131492	GM12878	blood:	n/a	n/a
31	POLR2A	chr2:209130547-209131416	MCF-7	breast:	n/a	n/a
32	MAX	chr2:209130545-209130895	K562	blood:	n/a	n/a
33	SP1	chr2:209129960-209131238	HCT-116	colon:	n/a	chr2:209130960-209130973 chr2:209130951-209130963
34	POLR2A	chr2:209130466-209131378	GM12878	blood:	n/a	n/a
35	PML	chr2:209130466-209131130	K562	blood:	n/a	n/a
36	FOXA1	chr2:209130540-209131037	T-47D	breast:	n/a	n/a
37	HNF4A	chr2:209130518-209131212	HepG2	liver:	n/a	chr2:209130751-209130758 chr2:209130747-209130763
38	BACH1	chr2:209130552-209130932	H1-hESC	embryonic stem cell:	n/a	n/a
39	MAX	chr2:209130391-209131254	MCF-7	breast:	n/a	n/a
40	NR3C1	chr2:209130549-209130905	A549	lung:	n/a	n/a
41	TCF12	chr2:209130612-209130912	H1-hESC	embryonic stem cell:	n/a	n/a
42	ELK1	chr2:209130531-209131114	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:209129908-209131339	ProgFib	skin:	n/a	n/a
44	HNF4A	chr2:209130508-209131154	HepG2	liver:	n/a	chr2:209130751-209130758 chr2:209130747-209130763
45	POLR2A	chr2:209129665-209132065	GM12891	blood:	n/a	n/a
46	ELF1	chr2:209130488-209131208	HepG2	liver:	n/a	n/a
47	POLR2A	chr2:209130046-209131501	GM15510	blood:	n/a	n/a
48	SMC3	chr2:209130745-209130896	K562	blood:	n/a	n/a
49	FOXA2	chr2:209130562-209131166	A549	lung:	n/a	n/a
50	ZNF143	chr2:209130297-209131557	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:209130521..209131243-chr8:23314842..23315390,2	Hela-S3	cervix:
2	chr1:28832504..28833487-chr2:209130651..209131371,2	Hela-S3	cervix:
3	chr2:209129671..209132812-chr2:209132994..209136144,5	MCF-7	breast:
4	chr1:87793559..87794463-chr2:209130596..209131219,2	NB4	blood:
5	chr2:209119063..209119975-chr2:209130358..209131188,2	K562	blood:
6	chr2:209116323..209122695-chr2:209127326..209132568,14	K562	blood:
7	chr2:209119923..209123053-chr2:209129009..209130826,3	MCF-7	breast:
8	chr2:209116323..209123332-chr2:209127326..209134005,17	K562	blood:
9	chr2:209129669..209131681-chr2:209132251..209135245,2	K562	blood:
10	chr2:209119136..209119874-chr2:209130641..209131606,2	MCF-7	breast:
11	chr2:209117138..209121626-chr2:209129108..209132782,7	MCF-7	breast:

No data

Variant related genes	Relation type
PIKFYVE	TF binding region
ENSG00000228380	Chromatin interaction
ENSG00000143013	Chromatin interaction
ENSG00000138413	Chromatin interaction
ENSG00000242125	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000197217	Chromatin interaction
ENSG00000231908	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10174541	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10186350	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10194539	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10198535	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10202116	1.00[ASN][1000 genomes]
rs10497897	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10497898	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11554137	1.00[ASN][1000 genomes]
rs11685614	1.00[ASN][1000 genomes]
rs11885913	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11895188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11898653	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11901959	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12694100	0.91[EUR][1000 genomes]
rs12694101	0.96[EUR][1000 genomes]
rs13412043	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17699838	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1866046	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34218846	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3928183	1.00[ASN][1000 genomes]
rs59522113	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59684347	1.00[ASN][1000 genomes]
rs6435435	1.00[ASN][1000 genomes]
rs66826643	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs66887797	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67202912	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6725418	0.96[EUR][1000 genomes]
rs6725527	0.80[EUR][1000 genomes]
rs67581965	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67669827	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72976889	1.00[ASN][1000 genomes]
rs72989243	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73056463	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73070950	1.00[ASN][1000 genomes]
rs73070958	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73070962	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557303	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7609093	0.90[AFR][1000 genomes]
rs9646838	0.82[AFR][1000 genomes];1.00[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	nsv1010531	chr2:208610639-209176782	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv536130	chr2:208610639-209176782	Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv534496	chr2:208814372-209302791	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	nsv834517	chr2:209006797-209170269	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv584297	chr2:209020181-209316760	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr2:209129600-209130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr2:209129600-209130800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:209129600-209132000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:209129800-209130800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr2:209129800-209130800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr2:209129800-209130800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr2:209129800-209130800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr2:209129800-209130800	Flanking Active TSS	NHDF-Ad	bronchial
9	chr2:209129800-209131400	Active TSS	Colonic Mucosa	Colon
10	chr2:209129800-209131600	Active TSS	Esophagus	oesophagus
11	chr2:209129800-209132800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr2:209129800-209132800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:209129800-209133000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr2:209129800-209133000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:209130000-209130800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:209130000-209130800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
17	chr2:209130000-209130800	Flanking Active TSS	HUVEC	blood vessel
18	chr2:209130000-209130800	Flanking Active TSS	NH-A	brain
19	chr2:209130000-209131800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:209130000-209132000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr2:209130000-209132200	Active TSS	Aorta	Aorta
22	chr2:209130000-209132200	Active TSS	Right Ventricle	heart
23	chr2:209130000-209132400	Active TSS	Psoas Muscle	Psoas
24	chr2:209130000-209132600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr2:209130000-209132600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:209130000-209132600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:209130000-209132800	Active TSS	H9 Cell Line	embryonic stem cell
28	chr2:209130000-209132800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:209130000-209132800	Active TSS	Ovary	ovary
30	chr2:209130200-209130800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr2:209130200-209131000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:209130200-209131600	Active TSS	Brain Angular Gyrus	brain
33	chr2:209130200-209131600	Active TSS	Brain Anterior Caudate	brain
34	chr2:209130200-209131600	Active TSS	Brain Cingulate Gyrus	brain
35	chr2:209130200-209131600	Active TSS	Pancreas	Pancrea
36	chr2:209130200-209131600	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr2:209130200-209131600	Active TSS	Rectal Smooth Muscle	rectum
38	chr2:209130200-209131800	Active TSS	Brain Germinal Matrix	brain
39	chr2:209130200-209131800	Active TSS	Brain Hippocampus Middle	brain
40	chr2:209130200-209131800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr2:209130200-209131800	Active TSS	Brain Substantia Nigra	brain
42	chr2:209130200-209131800	Active TSS	Gastric	stomach
43	chr2:209130200-209131800	Active TSS	Left Ventricle	heart
44	chr2:209130200-209131800	Active TSS	Placenta Amnion	Placenta Amnion
45	chr2:209130200-209132000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:209130200-209132000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr2:209130200-209132000	Active TSS	Fetal Muscle Trunk	muscle
48	chr2:209130200-209132000	Bivalent/Poised TSS	HepG2	liver
49	chr2:209130200-209132200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:209130200-209132200	Active TSS	Fetal Intestine Small	intestine

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