Variant report

Variant	rs3757327
Chromosome Location	chr6:30027413-30027414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:30027402-30027435	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:30027015..30030813-chr6:30040823..30045193,4	K562	blood:
2	chr6:30001672..30004034-chr6:30026395..30027961,2	K562	blood:
3	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-AS1	TF binding region
ZNRD1	TF binding region
ENSG00000204618	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000231074	Chromatin interaction

Extended variants
information (count: 173 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:170)

rs_ID	r²[population]
rs1048412	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17187210	0.94[AFR][1000 genomes]
rs2074479	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2074480	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2074481	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2074482	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2286405	0.96[AFR][1000 genomes]
rs2301753	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2301754	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2394256	0.96[AFR][1000 genomes]
rs2394257	0.88[AFR][1000 genomes]
rs3734835	0.96[AFR][1000 genomes]
rs3757329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3757331	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765604	0.96[AFR][1000 genomes]
rs3765606	0.96[AFR][1000 genomes]
rs3869067	0.96[AFR][1000 genomes]
rs3869068	0.96[AFR][1000 genomes]
rs3893530	0.95[AFR][1000 genomes]
rs4448133	0.96[AFR][1000 genomes]
rs6457139	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457140	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6457141	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6902691	0.93[AFR][1000 genomes]
rs6905157	0.96[AFR][1000 genomes]
rs6910507	0.92[AFR][1000 genomes]
rs6910517	0.94[AFR][1000 genomes]
rs6910898	0.94[AFR][1000 genomes]
rs6911279	0.94[AFR][1000 genomes]
rs6911467	0.96[AFR][1000 genomes]
rs6911634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911724	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6911737	0.94[AFR][1000 genomes]
rs6912080	0.94[AFR][1000 genomes]
rs6912154	0.93[AFR][1000 genomes]
rs6912877	0.87[AFR][1000 genomes]
rs6917477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917603	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6919617	0.96[AFR][1000 genomes]
rs6922640	0.94[AFR][1000 genomes]
rs6926792	0.96[AFR][1000 genomes]
rs6930993	0.94[AFR][1000 genomes]
rs6931776	0.96[AFR][1000 genomes]
rs6941318	0.94[AFR][1000 genomes]
rs7738475	0.96[AFR][1000 genomes]
rs7742417	0.96[AFR][1000 genomes]
rs7742871	0.94[AFR][1000 genomes]
rs7746866	0.96[AFR][1000 genomes]
rs7750514	0.93[AFR][1000 genomes]
rs7751116	0.96[AFR][1000 genomes]
rs7758512	0.96[AFR][1000 genomes]
rs7760299	0.96[AFR][1000 genomes]
rs7761314	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7768179	0.85[AFR][1000 genomes]
rs7769930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770811	0.80[AFR][1000 genomes]
rs886997	0.83[AFR][1000 genomes]
rs9260951	0.92[AFR][1000 genomes]
rs9260959	0.87[AFR][1000 genomes]
rs9260960	0.94[AFR][1000 genomes]
rs9260961	0.94[AFR][1000 genomes]
rs9260963	0.94[AFR][1000 genomes]
rs9260964	0.94[AFR][1000 genomes]
rs9260965	0.94[AFR][1000 genomes]
rs9260966	0.94[AFR][1000 genomes]
rs9260967	0.94[AFR][1000 genomes]
rs9260968	0.94[AFR][1000 genomes]
rs9260970	0.94[AFR][1000 genomes]
rs9260971	0.94[AFR][1000 genomes]
rs9260972	0.94[AFR][1000 genomes]
rs9260974	0.94[AFR][1000 genomes]
rs9260975	0.94[AFR][1000 genomes]
rs9260977	0.94[AFR][1000 genomes]
rs9260978	0.94[AFR][1000 genomes]
rs9260979	0.94[AFR][1000 genomes]
rs9260980	0.93[AFR][1000 genomes]
rs9260982	0.94[AFR][1000 genomes]
rs9260987	0.91[AFR][1000 genomes]
rs9260990	0.92[AFR][1000 genomes]
rs9260994	0.89[AFR][1000 genomes]
rs9260995	0.94[AFR][1000 genomes]
rs9260996	0.94[AFR][1000 genomes]
rs9260999	0.94[AFR][1000 genomes]
rs9261000	0.94[AFR][1000 genomes]
rs9261001	0.93[AFR][1000 genomes]
rs9261003	0.93[AFR][1000 genomes]
rs9261004	0.94[AFR][1000 genomes]
rs9261008	0.91[AFR][1000 genomes]
rs9261009	0.93[AFR][1000 genomes]
rs9261010	0.94[AFR][1000 genomes]
rs9261012	0.90[AFR][1000 genomes]
rs9261013	0.94[AFR][1000 genomes]
rs9261015	0.94[AFR][1000 genomes]
rs9261016	0.94[AFR][1000 genomes]
rs9261020	0.93[AFR][1000 genomes]
rs9261022	0.93[AFR][1000 genomes]
rs9261023	0.93[AFR][1000 genomes]
rs9261024	0.93[AFR][1000 genomes]
rs9261026	0.93[AFR][1000 genomes]
rs9261031	0.94[AFR][1000 genomes]
rs9261033	0.94[AFR][1000 genomes]
rs9261049	0.94[AFR][1000 genomes]
rs9261060	0.92[AFR][1000 genomes]
rs9261074	0.93[AFR][1000 genomes]
rs9261103	0.95[AFR][1000 genomes]
rs9261105	0.96[AFR][1000 genomes]
rs9261110	0.96[AFR][1000 genomes]
rs9261111	0.96[AFR][1000 genomes]
rs9261113	0.95[AFR][1000 genomes]
rs9261115	0.96[AFR][1000 genomes]
rs9261116	0.96[AFR][1000 genomes]
rs9261128	0.96[AFR][1000 genomes]
rs9261129	0.96[AFR][1000 genomes]
rs9261137	0.96[AFR][1000 genomes]
rs9261145	0.96[AFR][1000 genomes]
rs9261149	0.94[AFR][1000 genomes]
rs9261150	0.96[AFR][1000 genomes]
rs9261154	0.95[AFR][1000 genomes]
rs9261162	0.91[AFR][1000 genomes]
rs9261163	0.96[AFR][1000 genomes]
rs9261170	0.96[AFR][1000 genomes]
rs9261174	0.96[AFR][1000 genomes]
rs9261180	0.96[AFR][1000 genomes]
rs9261183	0.94[AFR][1000 genomes]
rs9261185	0.94[AFR][1000 genomes]
rs9261186	0.96[AFR][1000 genomes]
rs9261187	0.96[AFR][1000 genomes]
rs9261188	0.95[AFR][1000 genomes]
rs9261189	0.96[AFR][1000 genomes]
rs9261195	0.96[AFR][1000 genomes]
rs9261198	0.93[AFR][1000 genomes]
rs9261199	0.96[AFR][1000 genomes]
rs9261200	0.96[AFR][1000 genomes]
rs9261201	0.96[AFR][1000 genomes]
rs9261204	0.96[AFR][1000 genomes]
rs9261205	0.96[AFR][1000 genomes]
rs9261206	0.96[AFR][1000 genomes]
rs9261209	0.96[AFR][1000 genomes]
rs9261210	0.96[AFR][1000 genomes]
rs9261216	0.96[AFR][1000 genomes]
rs9261217	0.96[AFR][1000 genomes]
rs9261221	0.96[AFR][1000 genomes]
rs9261222	0.94[AFR][1000 genomes]
rs9261224	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261227	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261243	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261254	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261256	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261274	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261277	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261278	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9261282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9261291	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261292	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261294	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261295	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261297	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261298	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261299	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261300	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9261302	0.96[AFR][1000 genomes];0.82[EUR][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
rs3757327	ZNRD1	cis	lymphoblastoid	seeQTL
rs3757327	C6orf12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29975200-30027800	Weak transcription	Aorta	Aorta
2	chr6:29975600-30027800	Weak transcription	Right Ventricle	heart
3	chr6:29975800-30027800	Weak transcription	Gastric	stomach
4	chr6:29977200-30027600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr6:29977200-30027800	Weak transcription	Fetal Intestine Small	intestine
6	chr6:29979000-30027600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr6:29979800-30027800	Weak transcription	Pancreas	Pancrea
8	chr6:29988200-30027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:29988200-30027800	Weak transcription	Esophagus	oesophagus
10	chr6:29988400-30027800	Weak transcription	Thymus	Thymus
11	chr6:29998000-30027600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr6:30001200-30027800	Weak transcription	Fetal Kidney	kidney
13	chr6:30006200-30027600	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:30011000-30027800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr6:30012600-30027800	Weak transcription	Small Intestine	intestine
16	chr6:30012800-30027600	Weak transcription	NHDF-Ad	bronchial
17	chr6:30012800-30027800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:30012800-30027800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:30013000-30027600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr6:30013400-30027600	Weak transcription	NH-A	brain
21	chr6:30013600-30027600	Weak transcription	Hela-S3	cervix
22	chr6:30013600-30027800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:30013600-30027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:30014000-30028000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:30015600-30027600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:30016000-30027800	Weak transcription	Spleen	Spleen
27	chr6:30017000-30027600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:30017400-30028400	Weak transcription	Lung	lung
29	chr6:30018000-30027600	Weak transcription	Brain Germinal Matrix	brain
30	chr6:30020000-30027800	Weak transcription	Fetal Stomach	stomach
31	chr6:30020200-30027600	Weak transcription	HUVEC	blood vessel
32	chr6:30020200-30027800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:30020400-30028200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr6:30021400-30027600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr6:30021400-30027800	Weak transcription	Fetal Brain Female	brain
36	chr6:30022000-30027800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:30022400-30027600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr6:30023000-30027800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:30023400-30027600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:30023400-30027600	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:30023600-30027600	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr6:30023600-30027800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:30024400-30027800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:30024400-30027800	Weak transcription	Stomach Mucosa	stomach
45	chr6:30024600-30027600	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr6:30024800-30027800	Weak transcription	HSMMtube	muscle
47	chr6:30025200-30027600	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:30025200-30027600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr6:30025200-30027800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr6:30025200-30027800	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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