Variant report

Variant	rs3753789
Chromosome Location	chr1:86174814-86174815
allele	A/G
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	POLR2A	chr1:86173418-86175301	PANC-1	pancreas:	n/a	n/a
2	MAZ	chr1:86173603-86174918	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
3	POLR2A	chr1:86173014-86175215	GM12878	blood:	n/a	n/a
4	RCOR1	chr1:86173455-86174839	K562	blood:	n/a	n/a
5	FOXA2	chr1:86174567-86174871	A549	lung:	n/a	n/a
6	PML	chr1:86173473-86174890	GM12878	blood:	n/a	chr1:86174287-86174295
7	MTA3	chr1:86173506-86174834	GM12878	blood:	n/a	n/a
8	ARID3A	chr1:86174220-86174974	K562	blood:	n/a	n/a
9	POLR2A	chr1:86173645-86174940	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:86173584-86174828	Raji	blood:	n/a	n/a
11	MAX	chr1:86173810-86174854	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
12	ELF1	chr1:86174544-86174842	K562	blood:	n/a	n/a
13	MAX	chr1:86173648-86174932	A549	lung:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
14	MAX	chr1:86173491-86174834	HCT-116	colon:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
15	KAP1	chr1:86173608-86174835	HEK293	kidney:	n/a	chr1:86174287-86174295
16	HCFC1	chr1:86172692-86175343	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr1:86173391-86175011	PANC-1	pancreas:	n/a	n/a
18	TCF12	chr1:86173632-86174845	A549	lung:	n/a	n/a
19	POLR2A	chr1:86173660-86174957	SK-N-MC	brain:	n/a	n/a
20	MYC	chr1:86173592-86174967	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
21	MYC	chr1:86173667-86174886	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
22	SP1	chr1:86173789-86174895	A549	lung:	n/a	n/a
23	CTCF	chr1:86174680-86174830	GM12872	blood:	n/a	n/a
24	JUND	chr1:86173592-86175119	K562	blood:	n/a	n/a
25	MXI1	chr1:86173490-86174848	HepG2	liver:	n/a	n/a
26	MAX	chr1:86174529-86174830	K562	blood:	n/a	n/a
27	TBL1XR1	chr1:86173948-86175134	K562	blood:	n/a	n/a
28	HEY1	chr1:86173506-86174877	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:86173605-86174952	HEK293	kidney:	n/a	n/a
30	POLR2A	chr1:86173361-86174994	K562	blood:	n/a	n/a
31	CTCF	chr1:86173336-86175696	A549	lung:	n/a	n/a
32	CBX3	chr1:86173662-86174831	K562	blood:	n/a	n/a
33	FOXA2	chr1:86174484-86174837	A549	lung:	n/a	n/a
34	CTCF	chr1:86174740-86174890	NHEK	skin:	n/a	n/a
35	UBTF	chr1:86173646-86174903	K562	blood:	n/a	n/a
36	FOXA1	chr1:86174539-86174872	HepG2	liver:	n/a	n/a
37	CTCF	chr1:86173944-86175126	K562	blood:	n/a	n/a
38	IRF1	chr1:86173799-86174939	K562	blood:	n/a	chr1:86174367-86174379 chr1:86174750-86174767 chr1:86174367-86174380 chr1:86174367-86174379 chr1:86174750-86174762 chr1:86174366-86174380 chr1:86174751-86174762 chr1:86174750-86174762 chr1:86174368-86174379 chr1:86174749-86174763 chr1:86174750-86174763 chr1:86174367-86174384
39	POLR2A	chr1:86173514-86174814	K562	blood:	n/a	n/a
40	MAX	chr1:86173569-86174857	HCT-116	colon:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
41	MYC	chr1:86173821-86174817	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
42	POLR2A	chr1:86173577-86174821	Hela-S3	cervix:	n/a	n/a
43	ATF1	chr1:86174592-86175112	K562	blood:	n/a	n/a
44	BHLHE40	chr1:86173687-86174878	K562	blood:	n/a	n/a
45	RAD21	chr1:86173612-86174817	Hela-S3	cervix:	n/a	n/a
46	MYC	chr1:86173574-86175007	K562	blood:	n/a	chr1:86174061-86174070 chr1:86174061-86174076
47	POLR2A	chr1:86172636-86174928	GM12891	blood:	n/a	n/a
48	POLR2A	chr1:86173548-86174916	K562	blood:	n/a	n/a
49	ZNF143	chr1:86173864-86174924	K562	blood:	n/a	n/a
50	EP300	chr1:86173818-86175039	K562	blood:	n/a	n/a

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:

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

Extended variants
information (count: 65 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1047893	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10873717	0.82[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];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161654	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161656	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161657	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161658	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161659	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11161660	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161661	0.83[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	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161664	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11161665	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161667	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12058974	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12063702	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12075929	0.82[LWK][hapmap]
rs12089500	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12097932	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12128916	0.85[CEU][hapmap]
rs12564080	0.92[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12566746	0.92[CEU][hapmap];0.87[CHB][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12738010	0.88[ASN][1000 genomes]
rs12739713	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12752817	0.82[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	0.85[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1764285	0.85[CEU][hapmap]
rs1764291	0.85[CEU][hapmap]
rs1764292	0.85[CEU][hapmap]
rs1764299	0.85[CEU][hapmap]
rs1775988	0.85[CEU][hapmap]
rs1775990	0.88[CEU][hapmap]
rs1889919	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1889920	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2069208	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs2389972	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2995537	0.85[CEU][hapmap]
rs35438778	0.83[ASN][1000 genomes]
rs373787	0.85[CEU][hapmap]
rs3753786	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3753790	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	0.85[CEU][hapmap]
rs6576784	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6672312	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6689168	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697535	0.92[CEU][hapmap];0.87[CHB][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7518312	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7520491	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7532758	0.85[CEU][hapmap]
rs7554844	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs821386	0.89[CEU][hapmap]
rs821389	0.85[CEU][hapmap]
rs952837	0.85[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3753789	C1orf181	cis	multi-tissue	Pritchard
rs3753789	ZNHIT6	cis	lymphoblastoid	seeQTL
rs3753789	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs3753789	ZNHIT6	cis	Artery Aorta	GTEx
rs3753789	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs3753789	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs3753789	ZNHIT6	cis	lung	GTEx
rs3753789	C1orf52	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86172400-86175000	Active TSS	A549	lung
2	chr1:86173000-86175000	Active TSS	Rectal Smooth Muscle	rectum
3	chr1:86173000-86175200	Active TSS	Fetal Kidney	kidney
4	chr1:86173200-86175000	Active TSS	Brain Substantia Nigra	brain
5	chr1:86173400-86175000	Active TSS	Stomach Smooth Muscle	stomach
6	chr1:86173400-86175200	Active TSS	Brain Angular Gyrus	brain
7	chr1:86173600-86175200	Active TSS	Duodenum Mucosa	Duodenum
8	chr1:86173600-86175200	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr1:86174400-86175000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr1:86174400-86175000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr1:86174400-86175000	Flanking Active TSS	Dnd41	blood
12	chr1:86174400-86175000	Flanking Active TSS	Hela-S3	cervix
13	chr1:86174400-86175000	Flanking Active TSS	NHEK	skin
14	chr1:86174400-86175200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:86174400-86175200	Enhancers	Small Intestine	intestine
16	chr1:86174400-86185800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:86174600-86175000	Enhancers	Primary T cells from cord blood	blood
18	chr1:86174600-86175000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:86174600-86175000	Flanking Active TSS	Brain Anterior Caudate	brain
20	chr1:86174600-86175000	Flanking Active TSS	Brain Germinal Matrix	brain
21	chr1:86174600-86175000	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr1:86174600-86175000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr1:86174600-86175000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:86174600-86175200	Flanking Active TSS	HepG2	liver
25	chr1:86174800-86175000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:86174800-86175000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:86174800-86175000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr1:86174800-86175000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:86174800-86175000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr1:86174800-86175000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr1:86174800-86175000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:86174800-86175000	Active TSS	Adipose Nuclei	Adipose
33	chr1:86174800-86175000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:86174800-86175000	Active TSS	K562	blood
35	chr1:86174800-86175200	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr1:86174800-86175200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr1:86174800-86175200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr1:86174800-86175200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:86174800-86175200	Enhancers	Fetal Intestine Large	intestine
40	chr1:86174800-86175200	Enhancers	Stomach Mucosa	stomach
41	chr1:86174800-86175400	Enhancers	Fetal Intestine Small	intestine

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