Variant report

Variant	rs62435775
Chromosome Location	chr6:146136415-146136416
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:262)
CpG islands
(count:61)
Chromatin interactive
region (count:8)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:262 , 50 per page) page: 1 2 3 4 5 6

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HDAC2	chr6:146135327-146136420	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:146135581-146136640	GM12878	blood:	n/a	n/a
3	CREB1	chr6:146135060-146136852	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:146135159-146136908	HepG2	liver:	n/a	n/a
5	USF1	chr6:146136146-146136584	H1-hESC	embryonic stem cell:	n/a	n/a
6	JUND	chr6:146135812-146136587	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3AK20	chr6:146135324-146136566	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr6:146135233-146136496	ProgFib	skin:	n/a	n/a
9	TCF7L2	chr6:146135099-146136595	HCT-116	colon:	n/a	n/a
10	POLR2A	chr6:146135171-146136617	GM12878	blood:	n/a	n/a
11	REST	chr6:146135712-146136509	PFSK-1	brain:	n/a	n/a
12	SMC3	chr6:146135793-146136723	Hela-S3	cervix:	n/a	n/a
13	MAX	chr6:146134989-146136626	A549	lung:	n/a	n/a
14	MAZ	chr6:146135145-146136498	HepG2	liver:	n/a	n/a
15	MAX	chr6:146134981-146136578	MCF-7	breast:	n/a	n/a
16	MAX	chr6:146134959-146136571	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr6:146134353-146136631	IMR90	lung:	n/a	n/a
18	CCNT2	chr6:146135335-146136599	K562	blood:	n/a	n/a
19	BACH1	chr6:146135967-146136475	H1-hESC	embryonic stem cell:	n/a	n/a
20	MYC	chr6:146136214-146136524	MCF-7	breast:	n/a	n/a
21	TAF1	chr6:146135298-146136607	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr6:146135410-146136425	HUVEC	blood vessel:	n/a	n/a
23	MYC	chr6:146135101-146136516	K562	blood:	n/a	n/a
24	KAP1	chr6:146134885-146136594	HEK293	kidney:	n/a	n/a
25	REST	chr6:146134766-146137388	H1-neurons	neurons:	n/a	chr6:146135688-146135708 chr6:146135692-146135705 chr6:146135569-146135582 chr6:146137142-146137162
26	POLR2A	chr6:146135067-146136561	NB4	blood:	n/a	n/a
27	POLR2A	chr6:146131654-146136799	K562	blood:	n/a	n/a
28	NR2F2	chr6:146135814-146136533	K562	blood:	n/a	chr6:146136022-146136037
29	PAX5	chr6:146135566-146136519	GM12878	blood:	n/a	chr6:146135931-146135950 chr6:146135886-146135895
30	BHLHE40	chr6:146134957-146136642	K562	blood:	n/a	chr6:146135593-146135609 chr6:146135734-146135750
31	TRIM28	chr6:146135798-146136443	K562	blood:	n/a	n/a
32	POLR2A	chr6:146135608-146136770	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr6:146135217-146136603	GM12892	blood:	n/a	n/a
34	MYC	chr6:146134997-146136733	K562	blood:	n/a	n/a
35	POLR2A	chr6:146135553-146136595	ECC-1	luminal epithelium:	n/a	n/a
36	POLR2A	chr6:146135084-146136595	HL-60	blood:	n/a	n/a
37	ZKSCAN1	chr6:146135841-146136553	Hela-S3	cervix:	n/a	n/a
38	CTCF	chr6:146136360-146136510	AoAF	blood vessel:	n/a	n/a
39	POLR2A	chr6:146134920-146136936	GM18505	blood:	n/a	n/a
40	POLR2A	chr6:146135192-146136663	HEK293	kidney:	n/a	n/a
41	POLR2A	chr6:146134906-146136791	K562	blood:	n/a	n/a
42	POLR2A	chr6:146134940-146136743	K562	blood:	n/a	n/a
43	SMC3	chr6:146136046-146136423	GM12878	blood:	n/a	n/a
44	SMARCB1	chr6:146135360-146136775	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr6:146135174-146136692	GM12892	blood:	n/a	n/a
46	CREB1	chr6:146135251-146136470	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr6:146135199-146136622	GM18526	blood:	n/a	n/a
48	POLR2A	chr6:146135169-146136517	Gliobla	brain:	n/a	n/a
49	POLR2A	chr6:146135681-146137042	SK-N-MC	brain:	n/a	n/a
50	JUND	chr6:146134307-146136784	K562	blood:	n/a	chr6:146134574-146134584

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:146136371-146136421	AG09309	skin:	n/a
2	chr6:146136371-146136421	HRCEpiC	kidney:	n/a
3	chr6:146136371-146136421	HAEpiC	amniotic membrane:	n/a
4	chr6:146136371-146136421	LNCaP	prostate:	n/a
5	chr6:146136371-146136421	MCF10A-Er-Src	breast:	n/a
6	chr6:146136371-146136421	T-47D	breast:	n/a
7	chr6:146136371-146136421	SAEC	small airway:	n/a
8	chr6:146136371-146136421	HPAEpiC	pulmonary alveolar:	n/a
9	chr6:146136371-146136421	CMK	blood:	n/a
10	chr6:146136371-146136421	GM19239	blood:	n/a
11	chr6:146136371-146136421	HCF	heart:	n/a
12	chr6:146136371-146136421	HRE	kidney:	n/a
13	chr6:146136371-146136421	NHDF-neo	bronchial:	n/a
14	chr6:146136371-146136421	ProgFib	skin:	n/a
15	chr6:146136371-146136421	NT2-D1	testis:	n/a
16	chr6:146136371-146136421	U87	brain:	n/a
17	chr6:146136371-146136421	AoSMC	blood vessel:	n/a
18	chr6:146136371-146136421	GM12878	blood:	n/a
19	chr6:146136371-146136421	ECC-1	luminal epithelium:	n/a
20	chr6:146136371-146136421	A549	lung:	n/a
21	chr6:146136371-146136421	AG04449	skin:	fetal
22	chr6:146136371-146136421	GM06990	blood:	n/a
23	chr6:146136371-146136421	Hepatocyte	liver:	n/a
24	chr6:146136371-146136421	HMEC	breast:	n/a
25	chr6:146136371-146136421	HCPEpiC	choroid plexus:	n/a
26	chr6:146136371-146136421	PFSK-1	brain:	n/a
27	chr6:146136371-146136421	HNPCEpiC	eye:	n/a
28	chr6:146136371-146136421	HUVEC	blood vessel:	n/a
29	chr6:146136371-146136421	SKMC	muscle:	n/a
30	chr6:146136371-146136421	HepG2	liver:	n/a
31	chr6:146136371-146136421	SK-N-SH_RA	brain:	n/a
32	chr6:146136371-146136421	HEK293	kidney:	embryo
33	chr6:146136371-146136421	RPTEC	kidney:	n/a
34	chr6:146136371-146136421	HCT-116	colon:	n/a
35	chr6:146136371-146136421	Caco-2	colon:	n/a
36	chr6:146136371-146136421	HEEpiC	esophagus:	n/a
37	chr6:146136371-146136421	AG09319	gingival:	n/a
38	chr6:146136371-146136421	AG10803	skin:	n/a
39	chr6:146136371-146136421	ovcar-3	ovarian:	n/a
40	chr6:146136371-146136421	PrEC	prostate:	n/a
41	chr6:146136371-146136421	IMR90	lung:	fetal
42	chr6:146136371-146136421	NB4	blood:	n/a
43	chr6:146136371-146136421	HRPEpiC	eye:	n/a
44	chr6:146136371-146136421	H1-hESC	embryonic stem cell:	embryo
45	chr6:146136371-146136421	MCF-7	breast:	n/a
46	chr6:146136371-146136421	HIPEpiC	eye:	n/a
47	chr6:146136371-146136421	K562	blood:	n/a
48	chr6:146136371-146136421	BJ	skin:	n/a
49	chr6:146136371-146136421	Jurkat	blood:	n/a
50	chr6:146136371-146136421	SK-N-MC	brain:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:146135125..146136955-chr9:136214416..136217085,2	MCF-7	breast:
2	chr6:146052168..146062191-chr6:146124046..146141258,59	K562	blood:
3	chr6:146054764..146058281-chr6:146133205..146137397,13	MCF-7	breast:
4	chr6:146133534..146136752-chr6:146283932..146287911,4	K562	blood:
5	chr6:146047378..146061811-chr6:146118130..146137627,77	K562	blood:
6	chr6:74230303..74231191-chr6:146136002..146136502,2	NB4	blood:
7	chr6:146055814..146058166-chr6:146135376..146138309,3	MCF-7	breast:
8	chr6:146136120..146137977-chr6:146284631..146286434,2	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRM1-1	chr6:146136377-146136567	ENSG00000235652
2	lnc-GRM1-1	chr6:146135923-146136599	NONHSAT115400
3	lnc-GRM1-1	chr6:146136012-146136567	NONHSAT115401
4	lnc-GRM1-1	chr6:146136012-146136567	NONHSAT115402
5	lnc-GRM1-1	chr6:146136048-146136567	ENSG00000235652.3

No data

Variant related genes	Relation type
FBXO30	TF binding region
ENSG00000235652	TF binding region
ENSG00000235652	CpG island
FBXO30	CpG island
ENSG00000148303	Chromatin interaction
ENSG00000148297	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000270828	Chromatin interaction
ENSG00000146414	Chromatin interaction
ENSG00000200831	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000206611	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1070518	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10872580	0.80[ASN][1000 genomes]
rs12199362	0.80[ASN][1000 genomes]
rs1415746	0.81[ASN][1000 genomes]
rs1415747	0.81[ASN][1000 genomes]
rs1890170	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1970306	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2142978	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2142980	1.00[ASN][1000 genomes]
rs2206142	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2223411	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2235481	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2246132	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2253757	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2265475	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2328709	0.80[ASN][1000 genomes]
rs2485631	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34541797	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3811102	0.80[ASN][1000 genomes]
rs4398765	0.83[ASN][1000 genomes]
rs4896838	0.86[ASN][1000 genomes]
rs4896844	0.81[ASN][1000 genomes]
rs6570713	0.81[ASN][1000 genomes]
rs6570732	0.87[ASN][1000 genomes]
rs6900175	0.89[ASN][1000 genomes]
rs6906258	0.80[ASN][1000 genomes]
rs6906402	0.80[ASN][1000 genomes]
rs6912351	0.81[AFR][1000 genomes]
rs6915718	0.80[ASN][1000 genomes]
rs6931553	0.80[ASN][1000 genomes]
rs702316	0.88[ASN][1000 genomes]
rs702318	0.86[ASN][1000 genomes]
rs702319	0.86[ASN][1000 genomes]
rs702322	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs702324	0.86[ASN][1000 genomes]
rs7746618	0.82[AFR][1000 genomes]
rs7752286	0.81[ASN][1000 genomes]
rs7753273	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9373467	0.84[EUR][1000 genomes]
rs9373475	0.80[ASN][1000 genomes]
rs9376965	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9386132	0.80[ASN][1000 genomes]
rs9386134	0.80[ASN][1000 genomes]
rs9386136	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390356	0.80[ASN][1000 genomes]
rs9403739	0.85[ASN][1000 genomes]
rs9485017	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9497403	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[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	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 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	chr6:146131200-146137000	Active TSS	GM12878-XiMat	blood
2	chr6:146132600-146136800	Active TSS	K562	blood
3	chr6:146132800-146137000	Active TSS	Colon Smooth Muscle	Colon
4	chr6:146132800-146137400	Active TSS	A549	lung
5	chr6:146133000-146136800	Active TSS	Hela-S3	cervix
6	chr6:146133000-146136800	Active TSS	HSMMtube	muscle
7	chr6:146133000-146136800	Active TSS	NHLF	lung
8	chr6:146133000-146137000	Active TSS	Ovary	ovary
9	chr6:146133200-146136800	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:146133200-146137000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:146133200-146137000	Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr6:146133200-146137000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:146133200-146137200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr6:146133400-146136800	Active TSS	Rectal Smooth Muscle	rectum
15	chr6:146133400-146137000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr6:146133400-146137000	Active TSS	Psoas Muscle	Psoas
17	chr6:146133400-146137200	Active TSS	H1 Cell Line	embryonic stem cell
18	chr6:146133600-146136800	Active TSS	Brain Germinal Matrix	brain
19	chr6:146133600-146136800	Active TSS	NHDF-Ad	bronchial
20	chr6:146133600-146137000	Active TSS	Aorta	Aorta
21	chr6:146133600-146137400	Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:146133600-146137400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:146133800-146136800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:146133800-146136800	Active TSS	Muscle Satellite Cultured Cells	--
25	chr6:146133800-146137000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:146133800-146137000	Active TSS	Fetal Stomach	stomach
27	chr6:146133800-146137000	Active TSS	HSMM	muscle
28	chr6:146133800-146137000	Active TSS	NHEK	skin
29	chr6:146133800-146137200	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr6:146133800-146137200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr6:146133800-146137400	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr6:146134000-146136800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr6:146134000-146136800	Active TSS	HepG2	liver
34	chr6:146134000-146137000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr6:146134000-146137000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:146134000-146137000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr6:146134000-146137000	Active TSS	Fetal Kidney	kidney
38	chr6:146134000-146137200	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr6:146134000-146137200	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr6:146134200-146136600	Active TSS	Brain Substantia Nigra	brain
41	chr6:146134200-146136800	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr6:146134200-146136800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:146134200-146136800	Active TSS	Fetal Heart	heart
44	chr6:146134200-146136800	Active TSS	Fetal Intestine Large	intestine
45	chr6:146134200-146136800	Active TSS	Fetal Muscle Leg	muscle
46	chr6:146134200-146137000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:146134200-146137000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr6:146134200-146137000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:146134200-146137000	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr6:146134200-146137000	Active TSS	Brain Anterior Caudate	brain

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