Variant report

Variant	rs3753790
Chromosome Location	chr1:86174772-86174773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:61)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:86173418-86175301	PANC-1	pancreas:	n/a	n/a
2	CTCF	chr1:86174660-86174810	HCT-116	colon:	n/a	n/a
3	E2F6	chr1:86173698-86174793	K562	blood:	n/a	n/a
4	MAZ	chr1:86173603-86174918	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
5	POLR2A	chr1:86173014-86175215	GM12878	blood:	n/a	n/a
6	RCOR1	chr1:86173455-86174839	K562	blood:	n/a	n/a
7	CTCF	chr1:86174640-86174790	K562	blood:	n/a	n/a
8	POLR2A	chr1:86173862-86174801	HCT-116	colon:	n/a	n/a
9	FOXA2	chr1:86174567-86174871	A549	lung:	n/a	n/a
10	PML	chr1:86173473-86174890	GM12878	blood:	n/a	chr1:86174287-86174295
11	MTA3	chr1:86173506-86174834	GM12878	blood:	n/a	n/a
12	FOXA2	chr1:86174628-86174775	HepG2	liver:	n/a	n/a
13	ARID3A	chr1:86174220-86174974	K562	blood:	n/a	n/a
14	POLR2A	chr1:86173645-86174940	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr1:86173584-86174828	Raji	blood:	n/a	n/a
16	MAX	chr1:86173810-86174854	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
17	ELF1	chr1:86174544-86174842	K562	blood:	n/a	n/a
18	MAX	chr1:86173648-86174932	A549	lung:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
19	MAX	chr1:86173491-86174834	HCT-116	colon:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
20	KAP1	chr1:86173608-86174835	HEK293	kidney:	n/a	chr1:86174287-86174295
21	CTCF	chr1:86174640-86174790	HMEC	breast:	n/a	n/a
22	HCFC1	chr1:86172692-86175343	Hela-S3	cervix:	n/a	n/a
23	CTCF	chr1:86174664-86174806	K562	blood:	n/a	n/a
24	POLR2A	chr1:86174625-86174784	GM12878	blood:	n/a	n/a
25	POLR2A	chr1:86173391-86175011	PANC-1	pancreas:	n/a	n/a
26	TCF12	chr1:86173632-86174845	A549	lung:	n/a	n/a
27	POLR2A	chr1:86173660-86174957	SK-N-MC	brain:	n/a	n/a
28	MYC	chr1:86173592-86174967	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
29	MYC	chr1:86173667-86174886	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
30	SP1	chr1:86173789-86174895	A549	lung:	n/a	n/a
31	POLR2A	chr1:86173540-86174795	GM12878	blood:	n/a	n/a
32	CTCF	chr1:86174680-86174830	GM12872	blood:	n/a	n/a
33	JUND	chr1:86173592-86175119	K562	blood:	n/a	n/a
34	MXI1	chr1:86173490-86174848	HepG2	liver:	n/a	n/a
35	MAX	chr1:86174529-86174830	K562	blood:	n/a	n/a
36	POLR2A	chr1:86173714-86174799	K562	blood:	n/a	n/a
37	TBL1XR1	chr1:86173948-86175134	K562	blood:	n/a	n/a
38	HEY1	chr1:86173506-86174877	HepG2	liver:	n/a	n/a
39	ZBTB7A	chr1:86174580-86174811	K562	blood:	n/a	n/a
40	CTCF	chr1:86174640-86174790	WI-38	lung:	n/a	n/a
41	CTCF	chr1:86174678-86174803	Hela-S3	cervix:	n/a	n/a
42	POLR2A	chr1:86173605-86174952	HEK293	kidney:	n/a	n/a
43	POLR2A	chr1:86173361-86174994	K562	blood:	n/a	n/a
44	CTCF	chr1:86173336-86175696	A549	lung:	n/a	n/a
45	CBX3	chr1:86173662-86174831	K562	blood:	n/a	n/a
46	FOXA2	chr1:86174484-86174837	A549	lung:	n/a	n/a
47	CTCF	chr1:86174740-86174890	NHEK	skin:	n/a	n/a
48	UBTF	chr1:86173646-86174903	K562	blood:	n/a	n/a
49	EP300	chr1:86173993-86174776	A549	lung:	n/a	n/a
50	FOXA1	chr1:86174539-86174872	HepG2	liver:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:86174739-86174789	HCM	heart:	n/a
2	chr1:86174739-86174789	HEEpiC	esophagus:	n/a
3	chr1:86174739-86174789	T-47D	breast:	n/a
4	chr1:86174739-86174789	NT2-D1	testis:	n/a
5	chr1:86174739-86174789	ECC-1	luminal epithelium:	n/a
6	chr1:86174739-86174789	HAEpiC	amniotic membrane:	n/a
7	chr1:86174739-86174789	IMR90	lung:	fetal
8	chr1:86174739-86174789	ProgFib	skin:	n/a
9	chr1:86174739-86174789	SK-N-MC	brain:	n/a
10	chr1:86174739-86174789	HPAEpiC	pulmonary alveolar:	n/a
11	chr1:86174739-86174789	HUVEC	blood vessel:	n/a
12	chr1:86174739-86174789	GM19239	blood:	n/a
13	chr1:86174739-86174789	GM06990	blood:	n/a
14	chr1:86174739-86174789	BJ	skin:	n/a
15	chr1:86174739-86174789	PrEC	prostate:	n/a
16	chr1:86174739-86174789	GM12892	blood:	n/a
17	chr1:86174739-86174789	HRE	kidney:	n/a
18	chr1:86174739-86174789	MCF10A-Er-Src	breast:	n/a
19	chr1:86174739-86174789	Caco-2	colon:	n/a
20	chr1:86174739-86174789	HIPEpiC	eye:	n/a
21	chr1:86174739-86174789	SK-N-SH_RA	brain:	n/a
22	chr1:86174739-86174789	SAEC	small airway:	n/a
23	chr1:86174739-86174789	H1-hESC	embryonic stem cell:	embryo
24	chr1:86174739-86174789	SKMC	muscle:	n/a
25	chr1:86174739-86174789	HepG2	liver:	n/a
26	chr1:86174739-86174789	Hela-S3	cervix:	n/a
27	chr1:86174739-86174789	AG04449	skin:	fetal
28	chr1:86174739-86174789	HNPCEpiC	eye:	n/a
29	chr1:86174739-86174789	NHDF-neo	bronchial:	n/a
30	chr1:86174739-86174789	NB4	blood:	n/a
31	chr1:86174739-86174789	Jurkat	blood:	n/a
32	chr1:86174739-86174789	HRPEpiC	eye:	n/a
33	chr1:86174739-86174789	PFSK-1	brain:	n/a
34	chr1:86174739-86174789	HMEC	breast:	n/a
35	chr1:86174739-86174789	PANC-1	pancreas:	n/a
36	chr1:86174739-86174789	RPTEC	kidney:	n/a
37	chr1:86174739-86174789	ovcar-3	ovarian:	n/a
38	chr1:86174739-86174789	BE2_C	brain:	n/a
39	chr1:86174739-86174789	SK-N-SH	brain:	n/a
40	chr1:86174739-86174789	HCT-116	colon:	n/a
41	chr1:86174739-86174789	AG09319	gingival:	n/a
42	chr1:86174739-86174789	HRCEpiC	kidney:	n/a
43	chr1:86174739-86174789	AG10803	skin:	n/a
44	chr1:86174739-86174789	GM12878	blood:	n/a
45	chr1:86174739-86174789	Hepatocyte	liver:	n/a
46	chr1:86174739-86174789	AG04450	lung:	fetal
47	chr1:86174739-86174789	AG09309	skin:	n/a
48	chr1:86174739-86174789	MCF-7	breast:	n/a
49	chr1:86174739-86174789	GM12891	blood:	n/a
50	chr1:86174739-86174789	A549	lung:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:86043660..86051626-chr1:86167839..86177430,17	K562	blood:
2	chr1:86174243..86176856-chr1:86192936..86194526,2	K562	blood:
3	chr1:86046116..86050935-chr1:86168336..86177340,12	K562	blood:

No data

Variant related genes	Relation type
ZNHIT6	TF binding region
ZNHIT6	CpG island
ENSG00000272691	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1047893	0.92[CEU][hapmap];0.87[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1047895	0.85[CEU][hapmap]
rs10873716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873717	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161649	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11161650	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161654	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161656	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161657	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161658	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161659	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161660	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161661	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161662	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11161663	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161664	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161665	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161667	0.86[ASN][1000 genomes]
rs12058974	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12063702	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12089500	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12097932	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12128916	0.83[CEU][hapmap]
rs12564080	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12566746	0.93[CEU][hapmap];0.87[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12738010	0.88[ASN][1000 genomes]
rs12739713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12752817	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12756013	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12757270	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12758511	0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1539444	0.92[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1764285	0.85[CEU][hapmap]
rs1764291	0.83[CEU][hapmap]
rs1764292	0.83[CEU][hapmap]
rs1764299	0.83[CEU][hapmap]
rs1775988	0.85[CEU][hapmap]
rs1775990	0.85[CEU][hapmap]
rs1889919	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889920	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2069208	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2389972	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2995537	0.83[CEU][hapmap]
rs35438778	0.83[ASN][1000 genomes]
rs373787	0.83[CEU][hapmap]
rs3753786	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs418979	0.83[CEU][hapmap]
rs6576784	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6672312	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689168	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697535	0.93[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518312	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7520491	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7532758	0.85[CEU][hapmap]
rs7554844	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821386	0.86[CEU][hapmap]
rs821389	0.85[CEU][hapmap]
rs952837	0.83[CEU][hapmap]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3753790	ZNHIT6	cis	lung	GTEx
rs3753790	C1orf181	cis	multi-tissue	Pritchard
rs3753790	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs3753790	ZNHIT6	cis	Artery Aorta	GTEx
rs3753790	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs3753790	C1orf181	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86172000-86174800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:86172400-86174800	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr1:86172400-86174800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:86172400-86175000	Active TSS	A549	lung
5	chr1:86172600-86174800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:86172600-86174800	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:86172600-86174800	Active TSS	HSMM	muscle
8	chr1:86172600-86174800	Active TSS	HSMMtube	muscle
9	chr1:86172800-86174800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:86172800-86174800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr1:86172800-86174800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:86172800-86174800	Active TSS	Aorta	Aorta
13	chr1:86173000-86174800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:86173000-86174800	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr1:86173000-86174800	Active TSS	Osteobl	bone
16	chr1:86173000-86175000	Active TSS	Rectal Smooth Muscle	rectum
17	chr1:86173000-86175200	Active TSS	Fetal Kidney	kidney
18	chr1:86173200-86174800	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr1:86173200-86174800	Active TSS	NH-A	brain
20	chr1:86173200-86175000	Active TSS	Brain Substantia Nigra	brain
21	chr1:86173400-86174800	Active TSS	Psoas Muscle	Psoas
22	chr1:86173400-86174800	Active TSS	Sigmoid Colon	Sigmoid Colon
23	chr1:86173400-86175000	Active TSS	Stomach Smooth Muscle	stomach
24	chr1:86173400-86175200	Active TSS	Brain Angular Gyrus	brain
25	chr1:86173600-86175200	Active TSS	Duodenum Mucosa	Duodenum
26	chr1:86173600-86175200	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr1:86174200-86174800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:86174200-86174800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:86174200-86174800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
30	chr1:86174200-86174800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr1:86174200-86174800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:86174200-86174800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr1:86174200-86174800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:86174200-86174800	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr1:86174200-86174800	Flanking Active TSS	Liver	Liver
36	chr1:86174200-86174800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr1:86174400-86174800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr1:86174400-86174800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:86174400-86174800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:86174400-86174800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:86174400-86174800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:86174400-86174800	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr1:86174400-86174800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:86174400-86174800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr1:86174400-86174800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
46	chr1:86174400-86174800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:86174400-86174800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr1:86174400-86174800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:86174400-86174800	Flanking Active TSS	Fetal Heart	heart
50	chr1:86174400-86174800	Enhancers	Lung	lung

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