Variant report

Variant	rs6792510
Chromosome Location	chr3:48723302-48723303
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:405)
CpG islands
(count:61)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:405 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr3:48723237-48723511	K562	blood:	n/a	n/a
2	CTCF	chr3:48722664-48724339	A549	lung:	n/a	chr3:48723416-48723432
3	CTCF	chr3:48722948-48723622	Gliobla	brain:	n/a	chr3:48723416-48723432
4	POLR2A	chr3:48723037-48723681	PFSK-1	brain:	n/a	n/a
5	RAD21	chr3:48722881-48723577	HepG2	liver:	n/a	n/a
6	USF1	chr3:48723028-48723535	H1-hESC	embryonic stem cell:	n/a	n/a
7	CTCF	chr3:48722723-48723820	MCF-7	breast:	n/a	chr3:48723416-48723432
8	PAX5	chr3:48722990-48723593	GM12878	blood:	n/a	chr3:48723417-48723426 chr3:48723321-48723348
9	CTCF	chr3:48722931-48723612	MCF-7	breast:	n/a	chr3:48723416-48723432
10	POLR2A	chr3:48722958-48723386	H1-hESC	embryonic stem cell:	n/a	n/a
11	NRF1	chr3:48722884-48723544	GM12878	blood:	n/a	chr3:48723352-48723363
12	MYC	chr3:48723016-48723688	H1-hESC	embryonic stem cell:	n/a	chr3:48723332-48723341
13	ZBTB7A	chr3:48723256-48723725	K562	blood:	n/a	n/a
14	MAX	chr3:48722980-48723635	A549	lung:	n/a	chr3:48723332-48723341
15	POLR2A	chr3:48723054-48723483	K562	blood:	n/a	n/a
16	POLR2A	chr3:48722946-48724229	PANC-1	pancreas:	n/a	n/a
17	CEBPD	chr3:48722959-48723517	HepG2	liver:	n/a	n/a
18	RFX5	chr3:48723273-48723403	HepG2	liver:	n/a	n/a
19	MAFK	chr3:48723121-48723458	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr3:48722876-48723663	MCF-7	breast:	n/a	n/a
21	TAF1	chr3:48723111-48723531	SK-N-SH	brain:	n/a	n/a
22	RAD21	chr3:48722860-48723685	H1-hESC	embryonic stem cell:	n/a	n/a
23	GATA2	chr3:48723246-48723593	K562	blood:	n/a	n/a
24	NFIC	chr3:48722928-48723509	ECC-1	luminal epithelium:	n/a	n/a
25	HEY1	chr3:48723057-48723626	K562	blood:	n/a	chr3:48723414-48723429
26	CREB1	chr3:48722834-48723690	GM12878	blood:	n/a	n/a
27	POLR2A	chr3:48722857-48723936	H1-hESC	embryonic stem cell:	n/a	n/a
28	CHD2	chr3:48722903-48723568	H1-hESC	embryonic stem cell:	n/a	chr3:48723034-48723044
29	POLR2A	chr3:48723080-48723474	MCF10A-Er-Src	breast:	n/a	n/a
30	MYC	chr3:48722938-48723584	NB4	blood:	n/a	chr3:48723332-48723341
31	MAFK	chr3:48723244-48723444	HepG2	liver:	n/a	n/a
32	USF2	chr3:48723219-48723382	HepG2	liver:	n/a	n/a
33	CEBPD	chr3:48723148-48723355	HepG2	liver:	n/a	n/a
34	MAX	chr3:48722921-48723593	NB4	blood:	n/a	chr3:48723332-48723341
35	CTCF	chr3:48722914-48723716	MCF-7	breast:	n/a	chr3:48723416-48723432
36	POLR2A	chr3:48722996-48723520	A549	lung:	n/a	n/a
37	SIN3AK20	chr3:48722886-48723573	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr3:48723139-48723506	K562	blood:	n/a	n/a
39	FOXM1	chr3:48722779-48723635	GM12878	blood:	n/a	n/a
40	USF2	chr3:48722956-48723557	H1-hESC	embryonic stem cell:	n/a	n/a
41	GATA3	chr3:48723170-48723623	T-47D	breast:	n/a	n/a
42	BHLHE40	chr3:48723024-48723631	K562	blood:	n/a	n/a
43	E2F6	chr3:48723023-48723510	A549	lung:	n/a	chr3:48723046-48723058
44	POLR2A	chr3:48722908-48723468	HL-60	blood:	n/a	n/a
45	MAZ	chr3:48722902-48723918	GM12878	blood:	n/a	chr3:48723332-48723341
46	TAF1	chr3:48723047-48723360	Hela-S3	cervix:	n/a	n/a
47	POLR2A	chr3:48722910-48723641	GM12878	blood:	n/a	n/a
48	MYC	chr3:48722975-48723401	MCF-7	breast:	n/a	chr3:48723332-48723341
49	CTCF	chr3:48723280-48723430	RPTEC	kidney:	n/a	n/a
50	USF1	chr3:48723146-48723470	SK-N-SH_RA	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:48723293-48723343	NT2-D1	testis:	n/a
2	chr3:48723293-48723343	HCM	heart:	n/a
3	chr3:48723293-48723343	HCT-116	colon:	n/a
4	chr3:48723293-48723343	HCF	heart:	n/a
5	chr3:48723293-48723343	PrEC	prostate:	n/a
6	chr3:48723293-48723343	HIPEpiC	eye:	n/a
7	chr3:48723293-48723343	T-47D	breast:	n/a
8	chr3:48723293-48723343	SK-N-MC	brain:	n/a
9	chr3:48723293-48723343	HL-60	blood:	n/a
10	chr3:48723293-48723343	AG09319	gingival:	n/a
11	chr3:48723293-48723343	AG10803	skin:	n/a
12	chr3:48723293-48723343	GM12878	blood:	n/a
13	chr3:48723293-48723343	HRCEpiC	kidney:	n/a
14	chr3:48723293-48723343	BJ	skin:	n/a
15	chr3:48723293-48723343	SK-N-SH	brain:	n/a
16	chr3:48723293-48723343	IMR90	lung:	fetal
17	chr3:48723293-48723343	NH-A	brain:	n/a
18	chr3:48723293-48723343	HMEC	breast:	n/a
19	chr3:48723293-48723343	HEEpiC	esophagus:	n/a
20	chr3:48723293-48723343	BE2_C	brain:	n/a
21	chr3:48723293-48723343	GM12892	blood:	n/a
22	chr3:48723293-48723343	GM19239	blood:	n/a
23	chr3:48723293-48723343	NB4	blood:	n/a
24	chr3:48723293-48723343	MCF10A-Er-Src	breast:	n/a
25	chr3:48723293-48723343	MCF-7	breast:	n/a
26	chr3:48723293-48723343	NHDF-neo	bronchial:	n/a
27	chr3:48723293-48723343	GM06990	blood:	n/a
28	chr3:48723293-48723343	U87	brain:	n/a
29	chr3:48723293-48723343	K562	blood:	n/a
30	chr3:48723293-48723343	AG04449	skin:	fetal
31	chr3:48723293-48723343	PFSK-1	brain:	n/a
32	chr3:48723293-48723343	RPTEC	kidney:	n/a
33	chr3:48723293-48723343	Hela-S3	cervix:	n/a
34	chr3:48723293-48723343	ProgFib	skin:	n/a
35	chr3:48723293-48723343	AG04450	lung:	fetal
36	chr3:48723293-48723343	AG09309	skin:	n/a
37	chr3:48723293-48723343	HRE	kidney:	n/a
38	chr3:48723293-48723343	ECC-1	luminal epithelium:	n/a
39	chr3:48723293-48723343	Hepatocyte	liver:	n/a
40	chr3:48723293-48723343	SK-N-SH_RA	brain:	n/a
41	chr3:48723293-48723343	HRPEpiC	eye:	n/a
42	chr3:48723293-48723343	HepG2	liver:	n/a
43	chr3:48723293-48723343	SAEC	small airway:	n/a
44	chr3:48723293-48723343	LNCaP	prostate:	n/a
45	chr3:48723293-48723343	HCPEpiC	choroid plexus:	n/a
46	chr3:48723293-48723343	HAEpiC	amniotic membrane:	n/a
47	chr3:48723293-48723343	NHBE	bronchial:	n/a
48	chr3:48723293-48723343	PANC-1	pancreas:	n/a
49	chr3:48723293-48723343	SKMC	muscle:	n/a
50	chr3:48723293-48723343	Jurkat	blood:	n/a

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48646668..48648790-chr3:48722957..48725638,2	K562	blood:
2	chr3:48717662..48719232-chr3:48721596..48723446,2	MCF-7	breast:
3	chr3:48722838..48724823-chr3:48955919..48958463,2	K562	blood:
4	chr3:48700292..48701937-chr3:48721950..48724599,2	K562	blood:
5	chr3:48717071..48719987-chr3:48721738..48723845,3	MCF-7	breast:
6	chr3:48721678..48726571-chr3:48727447..48730865,5	K562	blood:
7	chr3:48699573..48703813-chr3:48719476..48724654,10	MCF-7	breast:
8	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
9	chr3:48720679..48723641-chr3:49054826..49057455,2	K562	blood:
10	chr3:48721882..48723836-chr3:48753260..48755276,2	K562	blood:
11	chr3:48720909..48723341-chr3:49022618..49025566,2	K562	blood:
12	chr12:54673175..54674036-chr3:48722962..48723585,2	NB4	blood:
13	chr3:48720678..48725638-chr3:48726169..48732697,10	MCF-7	breast:
14	chr3:48671184..48673366-chr3:48722826..48724747,2	K562	blood:
15	chr3:48713537..48717616-chr3:48720627..48724588,5	MCF-7	breast:
16	chr3:48722717..48723318-chr3:48802553..48803080,2	MCF-7	breast:
17	chr3:48700180..48704062-chr3:48721751..48723924,3	K562	blood:

No data

Variant related genes	Relation type
NCKIPSD	TF binding region
NCKIPSD	CpG island
ENSG00000010256	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000008300	Chromatin interaction
ENSG00000221883	Chromatin interaction
ENSG00000228350	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000273211	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000114302	Chromatin interaction
ENSG00000135486	Chromatin interaction
ENSG00000094916	Chromatin interaction
ENSG00000213672	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10865952	0.82[EUR][1000 genomes]
rs12493578	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12497850	0.83[EUR][1000 genomes]
rs1352420	0.82[EUR][1000 genomes]
rs4858798	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858828	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4858831	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6788650	0.83[EUR][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	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' 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	55 gene(s)	inside rSNPs	diseases
2	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv590248	chr3:48716993-48727636	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs6792510	NICN1-AS1	cis	Thyroid	GTEx
rs6792510	WDR6	cis	Whole Blood	GTEx
rs6792510	WDR6	cis	Esophagus Mucosa	GTEx
rs6792510	NCKIPSD	cis	Nerve Tibial	GTEx
rs6792510	AMT	cis	Muscle Skeletal	GTEx
rs6792510	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs6792510	NCKIPSD	cis	Whole Blood	GTEx
rs6792510	ARIH2	Cis_1M	lymphoblastoid	RTeQTL
rs6792510	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs6792510	CCDC36	cis	Artery Tibial	GTEx
rs6792510	NICN1	cis	Thyroid	GTEx
rs6792510	WDR6	cis	Adipose Subcutaneous	GTEx
rs6792510	NCKIPSD	cis	Muscle Skeletal	GTEx
rs6792510	WDR6	cis	Nerve Tibial	GTEx
rs6792510	WDR6	cis	lung	GTEx
rs6792510	WDR6	cis	Muscle Skeletal	GTEx
rs6792510	AMT	cis	Thyroid	GTEx
rs6792510	WDR6	cis	Artery Tibial	GTEx
rs6792510	WDR6	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48718800-48725600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:48720600-48724400	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr3:48721200-48723800	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr3:48721200-48724000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:48721600-48724000	Active TSS	Rectal Smooth Muscle	rectum
6	chr3:48721600-48724200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr3:48721800-48724000	Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr3:48721800-48724000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr3:48722000-48723800	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr3:48722000-48723800	Active TSS	Ovary	ovary
11	chr3:48722000-48724000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr3:48722200-48723600	Active TSS	Aorta	Aorta
13	chr3:48722200-48723800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:48722200-48723800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:48722200-48723800	Active TSS	Left Ventricle	heart
16	chr3:48722200-48723800	Active TSS	HepG2	liver
17	chr3:48722200-48724000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr3:48722400-48723600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:48722400-48723600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr3:48722400-48723600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:48722400-48723600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:48722400-48723600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr3:48722400-48723600	Active TSS	GM12878-XiMat	blood
24	chr3:48722400-48723800	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr3:48722400-48723800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:48722400-48723800	Active TSS	HSMM	muscle
27	chr3:48722400-48724000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr3:48722400-48724000	Active TSS	A549	lung
29	chr3:48722600-48723400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:48722600-48723400	Active TSS	Brain Inferior Temporal Lobe	brain
31	chr3:48722600-48723600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:48722600-48723600	Active TSS	Brain Angular Gyrus	brain
33	chr3:48722600-48723600	Active TSS	Fetal Kidney	kidney
34	chr3:48722600-48723600	Active TSS	Psoas Muscle	Psoas
35	chr3:48722600-48723600	Active TSS	Right Ventricle	heart
36	chr3:48722600-48723600	Active TSS	Hela-S3	cervix
37	chr3:48722600-48723600	Active TSS	NHLF	lung
38	chr3:48722600-48723800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr3:48722600-48723800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:48722600-48723800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:48722600-48723800	Active TSS	Brain Anterior Caudate	brain
42	chr3:48722600-48723800	Active TSS	Brain Cingulate Gyrus	brain
43	chr3:48722600-48723800	Active TSS	Brain Germinal Matrix	brain
44	chr3:48722600-48723800	Active TSS	Brain Hippocampus Middle	brain
45	chr3:48722600-48723800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:48722600-48723800	Active TSS	Brain Substantia Nigra	brain
47	chr3:48722600-48723800	Active TSS	Colon Smooth Muscle	Colon
48	chr3:48722600-48723800	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr3:48722600-48723800	Active TSS	Fetal Intestine Large	intestine
50	chr3:48722600-48723800	Active TSS	Fetal Lung	lung

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