Variant report

Variant	rs3757328
Chromosome Location	chr6:30028352-30028353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:91)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:91 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:30028324-30030090	MCF-7	breast:	n/a	n/a
2	POLR2A	chr6:30028331-30029541	Raji	blood:	n/a	n/a
3	POLR2A	chr6:30028318-30029641	K562	blood:	n/a	n/a
4	POLR2A	chr6:30028263-30029302	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr6:30028203-30030091	HepG2	liver:	n/a	n/a
6	POLR2A	chr6:30028288-30029795	Hela-S3	cervix:	n/a	n/a
7	EBF1	chr6:30028297-30029257	GM12878	blood:	n/a	chr6:30028684-30028695
8	POLR2A	chr6:30028273-30029658	H1-neurons	neurons:	n/a	n/a
9	MBD4	chr6:30028291-30030076	HepG2	liver:	n/a	n/a
10	TAF1	chr6:30028220-30029901	K562	blood:	n/a	n/a
11	MYC	chr6:30027984-30029471	A549	lung:	n/a	n/a
12	POLR2A	chr6:30028350-30029420	HUVEC	blood vessel:	n/a	n/a
13	MXI1	chr6:30028113-30030563	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr6:30028124-30030211	K562	blood:	n/a	n/a
15	MAX	chr6:30028331-30028694	K562	blood:	n/a	n/a
16	HEY1	chr6:30028341-30029361	K562	blood:	n/a	n/a
17	POLR2A	chr6:30028222-30029922	K562	blood:	n/a	n/a
18	JUND	chr6:30028062-30028367	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:30028350-30029249	GM12891	blood:	n/a	n/a
20	POLR2A	chr6:30028284-30030074	PFSK-1	brain:	n/a	n/a
21	MYC	chr6:30028308-30029879	NB4	blood:	n/a	n/a
22	POLR2A	chr6:30028259-30029880	HL-60	blood:	n/a	n/a
23	POLR2A	chr6:30028157-30030019	GM12892	blood:	n/a	n/a
24	POLR2A	chr6:30028294-30028620	H1-hESC	embryonic stem cell:	n/a	n/a
25	TAF1	chr6:30028351-30029417	K562	blood:	n/a	n/a
26	MTA3	chr6:30028085-30030162	GM12878	blood:	n/a	n/a
27	TBP	chr6:30028213-30029765	K562	blood:	n/a	n/a
28	PML	chr6:30028266-30029577	K562	blood:	n/a	n/a
29	POLR2A	chr6:30028257-30029393	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAX	chr6:30028336-30029616	ECC-1	luminal epithelium:	n/a	n/a
31	POLR2A	chr6:30028178-30029884	HL-60	blood:	n/a	n/a
32	POLR2A	chr6:30028227-30029811	GM12891	blood:	n/a	n/a
33	MAX	chr6:30028279-30029539	SK-N-SH	brain:	n/a	n/a
34	MYBL2	chr6:30028273-30029818	HepG2	liver:	n/a	n/a
35	MYC	chr6:30028337-30029566	K562	blood:	n/a	n/a
36	PML	chr6:30028222-30029626	K562	blood:	n/a	n/a
37	REST	chr6:30028216-30029469	HL-60	blood:	n/a	n/a
38	MYC	chr6:30028298-30029794	K562	blood:	n/a	n/a
39	TAF1	chr6:30028170-30029712	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr6:30028345-30029860	GM12891	blood:	n/a	n/a
41	RUNX3	chr6:30028299-30029932	GM12878	blood:	n/a	n/a
42	JUND	chr6:30028169-30030322	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr6:30028247-30029360	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr6:30028325-30029744	K562	blood:	n/a	n/a
45	POLR2A	chr6:30028283-30029714	HUVEC	blood vessel:	n/a	n/a
46	POLR2A	chr6:30028293-30029737	ProgFib	skin:	n/a	n/a
47	POLR2A	chr6:30028304-30030037	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:30028253-30029865	MCF-7	breast:	n/a	n/a
49	HEY1	chr6:30028098-30029885	K562	blood:	n/a	n/a
50	CBX3	chr6:30028132-30029252	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30028084..30030840-chr6:30103303..30105686,3	MCF-7	breast:
2	chr6:30028230..30030474-chr6:30075345..30077234,2	MCF-7	breast:
3	chr6:30027015..30030813-chr6:30040823..30045193,4	K562	blood:
4	chr17:59475970..59478357-chr6:30028344..30030119,2	MCF-7	breast:
5	chr6:30028283..30029937-chr6:30312414..30314218,2	K562	blood:
6	chr6:30002424..30006428-chr6:30027567..30030890,5	MCF-7	breast:
7	chr6:30028283..30030226-chr6:30312404..30313914,2	K562	blood:
8	chr6:30027269..30029063-chr6:30293187..30296080,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF39-4	chr6:30026145-30028756	ENSG00000204623

No data

Variant related genes	Relation type
ZNRD1	TF binding region
ZNRD1-AS1	TF binding region
ENSG00000204599	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000121068	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000204614	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000231074	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs10807060	0.95[AFR][1000 genomes]
rs10947040	0.92[AFR][1000 genomes]
rs10947042	0.94[AFR][1000 genomes]
rs10947043	0.96[AFR][1000 genomes]
rs10947045	0.93[AFR][1000 genomes]
rs10947046	0.96[AFR][1000 genomes]
rs10947047	0.96[AFR][1000 genomes]
rs11751331	0.85[AFR][1000 genomes]
rs11753431	0.96[AFR][1000 genomes]
rs11753939	0.96[AFR][1000 genomes]
rs11753957	0.95[AFR][1000 genomes]
rs11753960	0.96[AFR][1000 genomes]
rs11754605	0.96[AFR][1000 genomes]
rs11755337	0.85[AFR][1000 genomes]
rs11755374	0.85[AFR][1000 genomes]
rs11755549	0.96[AFR][1000 genomes]
rs11755961	0.85[AFR][1000 genomes]
rs11755966	0.85[AFR][1000 genomes]
rs11755984	0.85[AFR][1000 genomes]
rs11755992	0.85[AFR][1000 genomes]
rs11756025	0.81[AFR][1000 genomes]
rs11757750	0.84[AFR][1000 genomes]
rs11757792	0.85[AFR][1000 genomes]
rs11758493	0.85[AFR][1000 genomes]
rs11758516	0.83[AFR][1000 genomes]
rs11759388	0.96[AFR][1000 genomes]
rs11759891	0.84[AFR][1000 genomes]
rs11760176	0.88[AFR][1000 genomes]
rs11962771	0.96[AFR][1000 genomes]
rs11963840	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964113	0.96[AFR][1000 genomes]
rs11965379	0.96[AFR][1000 genomes]
rs11965452	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965458	0.96[AFR][1000 genomes]
rs11965524	0.96[AFR][1000 genomes]
rs11965540	0.96[AFR][1000 genomes]
rs11965585	0.96[AFR][1000 genomes]
rs11965659	0.96[AFR][1000 genomes]
rs11966447	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966449	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11967317	0.96[AFR][1000 genomes]
rs11967331	0.96[AFR][1000 genomes]
rs12110437	0.88[AFR][1000 genomes]
rs12111210	0.83[AFR][1000 genomes]
rs12661053	0.96[AFR][1000 genomes]
rs12661411	0.83[AFR][1000 genomes]
rs12661609	0.96[AFR][1000 genomes]
rs12662336	0.94[AFR][1000 genomes]
rs12662947	0.83[AFR][1000 genomes]
rs12662967	0.83[AFR][1000 genomes]
rs12663252	0.93[AFR][1000 genomes]
rs12663534	0.88[AFR][1000 genomes]
rs12664166	0.94[AFR][1000 genomes]
rs12664794	0.96[AFR][1000 genomes]
rs12664967	0.87[AFR][1000 genomes]
rs12665444	0.94[AFR][1000 genomes]
rs17180759	0.85[AFR][1000 genomes]
rs17180794	0.88[AFR][1000 genomes]
rs17180864	0.94[AFR][1000 genomes]
rs17186930	0.85[AFR][1000 genomes]
rs17186937	0.85[AFR][1000 genomes]
rs17186944	0.85[AFR][1000 genomes]
rs17186979	0.85[AFR][1000 genomes]
rs17187021	0.87[AFR][1000 genomes]
rs17187077	0.88[AFR][1000 genomes]
rs17187141	0.87[AFR][1000 genomes]
rs17187252	0.94[AFR][1000 genomes]
rs17187349	0.89[AFR][1000 genomes]
rs17187488	0.96[AFR][1000 genomes]
rs17187523	0.96[AFR][1000 genomes]
rs17193851	0.93[AFR][1000 genomes]
rs17193886	0.88[AFR][1000 genomes]
rs2275851	0.84[AFR][1000 genomes]
rs2285805	0.96[AFR][1000 genomes]
rs28570682	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28698859	0.94[AFR][1000 genomes]
rs2894006	0.80[AFR][1000 genomes]
rs3188482	0.96[AFR][1000 genomes]
rs34894339	0.86[AFR][1000 genomes]
rs35144883	0.85[AFR][1000 genomes]
rs35763150	0.93[AFR][1000 genomes]
rs3734830	0.85[AFR][1000 genomes]
rs3734833	0.85[AFR][1000 genomes]
rs3734834	0.82[AFR][1000 genomes]
rs3757333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765608	0.96[AFR][1000 genomes]
rs55760574	0.85[AFR][1000 genomes]
rs56015532	0.85[AFR][1000 genomes]
rs56052612	0.83[AFR][1000 genomes]
rs56216735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57035982	0.85[AFR][1000 genomes]
rs57080532	0.85[AFR][1000 genomes]
rs57680173	0.85[AFR][1000 genomes]
rs57799064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58161185	0.85[AFR][1000 genomes]
rs58314476	0.95[AFR][1000 genomes]
rs58555592	0.96[AFR][1000 genomes]
rs58858573	0.94[AFR][1000 genomes]
rs58867136	0.85[AFR][1000 genomes]
rs58980848	0.91[AFR][1000 genomes]
rs60265332	0.96[AFR][1000 genomes]
rs60477028	0.96[AFR][1000 genomes]
rs60587228	0.85[AFR][1000 genomes]
rs61704409	0.85[AFR][1000 genomes]
rs6457137	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6457138	0.93[AFR][1000 genomes]
rs6902901	0.96[AFR][1000 genomes]
rs6911583	0.94[AFR][1000 genomes]
rs6912001	0.96[AFR][1000 genomes]
rs6917877	0.92[AFR][1000 genomes]
rs6928966	0.96[AFR][1000 genomes]
rs6931672	0.96[AFR][1000 genomes]
rs6932091	0.96[AFR][1000 genomes]
rs6933897	0.96[AFR][1000 genomes]
rs6940552	0.96[AFR][1000 genomes]
rs6940956	0.94[AFR][1000 genomes]
rs72502507	0.92[AFR][1000 genomes]
rs72502509	0.94[AFR][1000 genomes]
rs73410515	0.82[AFR][1000 genomes]
rs73410518	0.94[AFR][1000 genomes]
rs73410524	0.87[AFR][1000 genomes]
rs73410525	0.92[AFR][1000 genomes]
rs73410528	0.94[AFR][1000 genomes]
rs73414461	0.94[AFR][1000 genomes]
rs73414465	0.96[AFR][1000 genomes]
rs73416498	0.95[AFR][1000 genomes]
rs73416501	0.96[AFR][1000 genomes]
rs73420421	0.96[AFR][1000 genomes]
rs73420434	0.96[AFR][1000 genomes]
rs73420439	0.96[AFR][1000 genomes]
rs73420484	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73428121	0.84[AFR][1000 genomes]
rs73428125	0.81[AFR][1000 genomes]
rs73428151	0.81[AFR][1000 genomes]
rs73428152	0.83[AFR][1000 genomes]
rs73725904	0.84[AFR][1000 genomes]
rs73725908	0.82[AFR][1000 genomes]
rs73725910	0.82[AFR][1000 genomes]
rs73725912	0.83[AFR][1000 genomes]
rs73725917	0.85[AFR][1000 genomes]
rs73725921	0.84[AFR][1000 genomes]
rs73725950	0.85[AFR][1000 genomes]
rs73725953	0.96[AFR][1000 genomes]
rs73725970	0.95[AFR][1000 genomes]
rs73725984	0.88[AFR][1000 genomes]
rs73728107	0.96[AFR][1000 genomes]
rs7742712	0.96[AFR][1000 genomes]
rs7742799	0.93[AFR][1000 genomes]
rs7746555	0.96[AFR][1000 genomes]
rs7750582	0.83[AFR][1000 genomes]
rs7762851	0.96[AFR][1000 genomes]
rs7764237	0.96[AFR][1000 genomes]
rs9261134	0.96[AFR][1000 genomes]
rs9261281	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9767125	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9767139	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031115	chr6:29934199-30058223	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv538172	chr6:29934199-30058223	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3757328	ZNRD1	cis	lymphoblastoid	seeQTL
rs3757328	ZNRD1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30017400-30028400	Weak transcription	Lung	lung
2	chr6:30027600-30028400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:30027600-30028400	Flanking Active TSS	Dnd41	blood
4	chr6:30027600-30028600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr6:30027600-30028600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:30027600-30028800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:30027600-30028800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:30027600-30030200	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:30027600-30031000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:30027800-30028400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:30027800-30028400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr6:30027800-30028400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr6:30027800-30028400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr6:30027800-30028400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr6:30027800-30028400	Flanking Active TSS	Brain Cingulate Gyrus	brain
16	chr6:30027800-30028400	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr6:30027800-30028400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:30027800-30028400	Flanking Active TSS	Colon Smooth Muscle	Colon
19	chr6:30027800-30028400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr6:30027800-30028400	Flanking Active TSS	Fetal Brain Female	brain
21	chr6:30027800-30028400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr6:30027800-30028400	Flanking Active TSS	Fetal Lung	lung
23	chr6:30027800-30028400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
24	chr6:30027800-30028400	Flanking Active TSS	Rectal Smooth Muscle	rectum
25	chr6:30027800-30028400	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr6:30027800-30028400	Enhancers	Spleen	Spleen
27	chr6:30027800-30028400	Flanking Active TSS	Hela-S3	cervix
28	chr6:30027800-30028400	Flanking Active TSS	HSMM	muscle
29	chr6:30027800-30028400	Flanking Active TSS	NH-A	brain
30	chr6:30027800-30028400	Flanking Active TSS	Osteobl	bone
31	chr6:30027800-30028600	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr6:30027800-30028600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr6:30027800-30028600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr6:30027800-30028600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr6:30027800-30028600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr6:30027800-30028600	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr6:30027800-30028600	Flanking Active TSS	Fetal Muscle Leg	muscle
38	chr6:30027800-30028600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr6:30027800-30028600	Flanking Active TSS	HUVEC	blood vessel
40	chr6:30027800-30028600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr6:30027800-30028800	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr6:30027800-30028800	Flanking Active TSS	Adipose Nuclei	Adipose
43	chr6:30027800-30028800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr6:30027800-30029400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:30027800-30029600	Active TSS	Right Atrium	heart
46	chr6:30027800-30029800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr6:30027800-30029800	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr6:30027800-30029800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr6:30027800-30029800	Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr6:30027800-30030000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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