Variant report

Variant	rs12654
Chromosome Location	chr6:34250202-34250203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:34249917..34252313-chr6:34359035..34361576,2	MCF-7	breast:
2	chr6:34250015..34252529-chr6:34278374..34280844,2	K562	blood:
3	chr6:34204158..34206160-chr6:34249084..34250799,2	K562	blood:
4	chr6:34202426..34206348-chr6:34246132..34251181,8	K562	blood:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMGA1-2	chr6:34247482-34252266	ENSG00000225339
2	lnc-HMGA1-2	chr6:34246917-34254539	NONHSAT112121
3	lnc-HMGA1-2	chr6:34247456-34254545	ENSG00000225339.2
4	lnc-HMGA1-2	chr6:34249692-34250339	ENSG00000225339.2

No data

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction
ENSG00000137309	Chromatin interaction

Extended variants
information (count: 60 )
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]
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]
rs56039915	1.00[AFR][1000 genomes];1.00[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:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12654	NUDT3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr6:34238400-34259400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:34240200-34255200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:34240400-34251800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:34240400-34255000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:34240400-34259800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:34240400-34259800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr6:34240600-34250400	Weak transcription	Brain Substantia Nigra	brain
10	chr6:34240600-34269200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr6:34240800-34261000	Weak transcription	Fetal Kidney	kidney
12	chr6:34241400-34260000	Weak transcription	Esophagus	oesophagus
13	chr6:34241600-34250400	Weak transcription	Fetal Thymus	thymus
14	chr6:34241600-34252800	Weak transcription	Stomach Mucosa	stomach
15	chr6:34242000-34252800	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:34243600-34250800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr6:34243600-34252600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr6:34243600-34257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:34244200-34251800	Weak transcription	Brain Anterior Caudate	brain
20	chr6:34244200-34260000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:34244400-34256600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:34244400-34273400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:34244800-34251400	Weak transcription	Osteobl	bone
24	chr6:34244800-34251600	Weak transcription	NHEK	skin
25	chr6:34245000-34250600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr6:34245000-34259800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:34245000-34260000	Weak transcription	NH-A	brain
28	chr6:34245000-34262600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:34245000-34263400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr6:34245200-34252200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:34245200-34255000	Weak transcription	Ovary	ovary
32	chr6:34245200-34259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr6:34245200-34260800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:34245400-34253000	Strong transcription	Fetal Stomach	stomach
35	chr6:34245400-34260800	Weak transcription	Aorta	Aorta
36	chr6:34245600-34250400	Strong transcription	Primary T cells from cord blood	blood
37	chr6:34245600-34251400	Weak transcription	HepG2	liver
38	chr6:34245600-34255200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr6:34245600-34257400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr6:34245600-34261600	Weak transcription	Gastric	stomach
41	chr6:34245800-34254800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:34245800-34255000	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:34245800-34260000	Weak transcription	HSMMtube	muscle
44	chr6:34246000-34251800	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr6:34246000-34253800	Strong transcription	Fetal Muscle Trunk	muscle
46	chr6:34246000-34264400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr6:34246200-34250800	Strong transcription	Fetal Muscle Leg	muscle
48	chr6:34246200-34252000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:34246600-34252600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:34246600-34256800	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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