Variant report

Variant	rs56039915
Chromosome Location	chr6:34247189-34247190
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:34247032-34247225	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:34246504-34247453	K562	blood:	n/a	n/a
3	POLR2A	chr6:34244327-34250971	K562	blood:	n/a	n/a
4	POLR2A	chr6:34246662-34247314	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:34246568-34247365	K562	blood:	n/a	n/a
6	POLR2A	chr6:34246943-34247197	H1-neurons	neurons:	n/a	n/a
7	POLR2A	chr6:34246646-34247260	HL-60	blood:	n/a	n/a
8	POLR2A	chr6:34246869-34247563	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:34211942..34216855-chr6:34244859..34247946,7	K562	blood:
2	chr6:34214507..34216888-chr6:34245546..34249056,4	K562	blood:
3	chr6:34202426..34206348-chr6:34246132..34251181,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGA1-2	chr6:34246917-34249243	NONHSAT112120
2	lnc-HMGA1-2	chr6:34246917-34254539	NONHSAT112121

No data

Variant related genes	Relation type
ENSG00000225339	TF binding region
ENSG00000186577	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10484267	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10484268	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1057691	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060308	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10648	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1127084	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1265	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13466	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883137	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883475	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883896	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16888452	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17628798	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17628946	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629180	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17629270	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696583	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696774	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17696829	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1994923	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs206922	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798554	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798557	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269032	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41269034	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269038	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55684754	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55694290	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55763242	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779010	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55798596	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55812200	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55833185	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55863933	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55864834	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56033036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56107559	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56188036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56274913	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56309550	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56323997	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56330729	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59832183	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes]
rs6911272	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738665	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7760373	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7770443	0.84[EUR][1000 genomes]
rs875274	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9368811	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885781	chr6:34110257-34247661	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv462903	chr6:34110257-34263743	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv602863	chr6:34110257-34263743	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
7	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
8	esv3377596	chr6:34243274-34247372	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56039915	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34218200-34255000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr6:34233000-34251800	Weak transcription	NHDF-Ad	bronchial
3	chr6:34234200-34247600	Weak transcription	Brain Germinal Matrix	brain
4	chr6:34238400-34259400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:34239000-34247600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr6:34240200-34249000	Weak transcription	NHLF	lung
7	chr6:34240200-34250200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr6:34240200-34255200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:34240400-34249600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:34240400-34251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:34240400-34255000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr6:34240400-34259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr6:34240400-34259800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:34240600-34247200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:34240600-34250400	Weak transcription	Brain Substantia Nigra	brain
16	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr6:34240800-34261000	Weak transcription	Fetal Kidney	kidney
18	chr6:34241000-34248600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr6:34241400-34260000	Weak transcription	Esophagus	oesophagus
20	chr6:34241600-34249600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:34241600-34250400	Weak transcription	Fetal Thymus	thymus
22	chr6:34241600-34252800	Weak transcription	Stomach Mucosa	stomach
23	chr6:34241800-34247800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr6:34242000-34252800	Weak transcription	Colon Smooth Muscle	Colon
25	chr6:34242200-34249600	Weak transcription	HUVEC	blood vessel
26	chr6:34242200-34250200	Weak transcription	GM12878-XiMat	blood
27	chr6:34243200-34248400	Enhancers	Psoas Muscle	Psoas
28	chr6:34243400-34247400	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr6:34243600-34250800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr6:34243600-34252600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr6:34243600-34257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr6:34244000-34248200	Weak transcription	HSMM	muscle
33	chr6:34244200-34251800	Weak transcription	Brain Anterior Caudate	brain
34	chr6:34244200-34260000	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr6:34244400-34256600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr6:34244800-34249000	Weak transcription	Fetal Lung	lung
38	chr6:34244800-34251400	Weak transcription	Osteobl	bone
39	chr6:34244800-34251600	Weak transcription	NHEK	skin
40	chr6:34245000-34250000	Weak transcription	Placenta	Placenta
41	chr6:34245000-34250600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:34245000-34259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr6:34245000-34260000	Weak transcription	NH-A	brain
44	chr6:34245000-34262600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:34245000-34263400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr6:34245200-34252200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr6:34245200-34255000	Weak transcription	Ovary	ovary
48	chr6:34245200-34259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr6:34245200-34260800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:34245400-34248000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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