Variant report

Variant	rs2052990
Chromosome Location	chr6:36729779-36729780
allele	G/T
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:6)
LncRNA
region (count:0)
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	chr6:36729732-36729900	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36728360..36730961-chr6:36735132..36738093,3	K562	blood:
2	chr6:36725564..36727264-chr6:36727766..36730682,2	K562	blood:
3	chr6:36726753..36730019-chr6:36730894..36734737,3	K562	blood:
4	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
5	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
6	chr6:36670725..36674166-chr6:36726971..36730200,3	MCF-7	breast:

No data

Variant related genes	Relation type
CPNE5	TF binding region
ENSG00000124762	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1010790	0.90[EUR][1000 genomes]
rs1010791	0.90[EUR][1000 genomes]
rs1064827	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs171033	0.84[ASN][1000 genomes]
rs1864750	0.80[EUR][1000 genomes]
rs236436	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs236444	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4711464	0.89[ASN][1000 genomes]
rs6927504	0.89[ASN][1000 genomes]
rs763047	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763048	0.97[ASN][1000 genomes]
rs9380596	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394380	0.90[EUR][1000 genomes]
rs9462215	0.89[EUR][1000 genomes]

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	nsv1023171	chr6:36686935-36880899	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv538202	chr6:36686935-36880899	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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 target site	27 gene(s)	inside rSNPs	diseases
3	nsv1033261	chr6:36687424-36837315	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv524053	chr6:36695223-36747406	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36721800-36733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:36722800-36748200	Weak transcription	Fetal Kidney	kidney
3	chr6:36723800-36736200	Weak transcription	Right Atrium	heart
4	chr6:36724000-36736200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr6:36724800-36734400	Weak transcription	Right Ventricle	heart
6	chr6:36725600-36730000	Weak transcription	Spleen	Spleen
7	chr6:36725600-36733800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr6:36725800-36735400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:36726000-36736200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr6:36726600-36729800	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr6:36726800-36730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:36726800-36733800	Weak transcription	Pancreas	Pancrea
13	chr6:36727000-36730400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:36727000-36732000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr6:36727000-36732000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr6:36727000-36732000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:36727000-36732400	Weak transcription	Fetal Muscle Leg	muscle
18	chr6:36727000-36733400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:36727000-36733800	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:36727200-36734000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr6:36727200-36736400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:36727400-36735200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr6:36727400-36736200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:36727600-36732400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:36727600-36732800	Weak transcription	GM12878-XiMat	blood
26	chr6:36727600-36733000	Weak transcription	Colonic Mucosa	Colon
27	chr6:36728200-36730800	Strong transcription	Fetal Stomach	stomach
28	chr6:36728600-36732600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:36728600-36732800	Weak transcription	HSMMtube	muscle
30	chr6:36729000-36732800	Weak transcription	Primary B cells from cord blood	blood
31	chr6:36729000-36732800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr6:36729400-36732400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr6:36729600-36733000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:36729600-36733000	Weak transcription	Brain Hippocampus Middle	brain
35	chr6:36729600-36733000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr6:36729600-36733000	Weak transcription	Brain Substantia Nigra	brain
37	chr6:36729600-36733200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr6:36729600-36733200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr6:36729600-36733200	Weak transcription	Brain Angular Gyrus	brain
40	chr6:36729600-36733600	Weak transcription	Brain Anterior Caudate	brain

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