Variant report

Variant	rs9380596
Chromosome Location	chr6:36727503-36727504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr6:36727360-36727510	GM12864	blood:	n/a	n/a
2	CTCF	chr6:36726577-36727594	SK-N-SH	brain:	n/a	chr6:36727117-36727135 chr6:36727112-36727133 chr6:36727118-36727134
3	CTCF	chr6:36727391-36727519	GM12892	blood:	n/a	n/a
4	CTCF	chr6:36727440-36727590	HRPEpiC	eye:	n/a	n/a
5	CTCF	chr6:36727500-36727650	AG09309	skin:	n/a	n/a
6	CTCF	chr6:36727420-36727570	HCPEpiC	choroid plexus:	n/a	n/a
7	CTCF	chr6:36727400-36727550	GM12867	blood:	n/a	n/a
8	CTCF	chr6:36727480-36727630	HepG2	liver:	n/a	n/a
9	CTCF	chr6:36727380-36727530	HEK293	kidney:	n/a	n/a
10	CTCF	chr6:36727500-36727650	GM12871	blood:	n/a	n/a
11	CTCF	chr6:36727440-36727590	AG04450	lung:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36582648..36583548-chr6:36726442..36727575,5	MCF-7	breast:
2	chr6:36692117..36693169-chr6:36726597..36727520,3	MCF-7	breast:
3	chr6:36717692..36718483-chr6:36726667..36727520,2	K562	blood:
4	chr6:36589397..36591575-chr6:36726645..36728482,2	MCF-7	breast:
5	chr6:36589945..36592639-chr6:36726671..36728710,2	K562	blood:
6	chr6:36726638..36727646-chr6:36738357..36739663,3	K562	blood:
7	chr6:36727502..36729456-chr6:36733982..36738042,3	K562	blood:
8	chr6:36561839..36564756-chr6:36723772..36727529,4	MCF-7	breast:
9	chr6:36726753..36730019-chr6:36730894..36734737,3	K562	blood:
10	chr6:36590930..36591805-chr6:36726654..36727603,2	MCF-7	breast:
11	chr6:36692374..36694188-chr6:36726056..36729043,2	MCF-7	breast:
12	chr6:36645102..36656546-chr6:36717974..36730993,29	MCF-7	breast:
13	chr6:36644838..36653438-chr6:36718524..36730954,23	MCF-7	breast:
14	chr6:36590960..36591893-chr6:36725819..36727563,13	K562	blood:
15	chr6:36590919..36591472-chr6:36727065..36727610,2	MCF-7	breast:
16	chr6:36656125..36657871-chr6:36725735..36728109,2	MCF-7	breast:
17	chr6:36670725..36674166-chr6:36726971..36730200,3	MCF-7	breast:

No data

Variant related genes	Relation type
CPNE5	TF binding region
ENSG00000263894	Chromatin interaction
ENSG00000124762	Chromatin interaction
ENSG00000112081	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1010790	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs1010791	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs1064827	0.87[CEU][hapmap];0.84[CHB][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10807175	0.87[AFR][1000 genomes]
rs13203743	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs171033	0.84[ASN][1000 genomes]
rs1864750	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2052990	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs236444	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs236452	0.82[CEU][hapmap]
rs370687	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4711464	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4714009	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs6927504	0.89[ASN][1000 genomes]
rs763047	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs763048	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs916295	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs9394380	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs9462215	0.83[CEU][hapmap];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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36721400-36728600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:36721800-36733200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr6:36722800-36727600	Enhancers	Stomach Mucosa	stomach
4	chr6:36722800-36748200	Weak transcription	Fetal Kidney	kidney
5	chr6:36723800-36736200	Weak transcription	Right Atrium	heart
6	chr6:36724000-36728200	Weak transcription	Fetal Stomach	stomach
7	chr6:36724000-36736200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr6:36724800-36734400	Weak transcription	Right Ventricle	heart
9	chr6:36725200-36727600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:36725400-36727600	Enhancers	Primary B cells from peripheral blood	blood
11	chr6:36725600-36727600	Enhancers	GM12878-XiMat	blood
12	chr6:36725600-36727800	Enhancers	Primary B cells from cord blood	blood
13	chr6:36725600-36730000	Weak transcription	Spleen	Spleen
14	chr6:36725600-36733800	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr6:36725800-36728600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:36725800-36735400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr6:36726000-36736200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:36726400-36727600	Enhancers	Colonic Mucosa	Colon
19	chr6:36726600-36727600	Enhancers	Brain Cingulate Gyrus	brain
20	chr6:36726600-36727600	Bivalent Enhancer	HepG2	liver
21	chr6:36726600-36728000	Weak transcription	Esophagus	oesophagus
22	chr6:36726600-36729600	Enhancers	Brain Anterior Caudate	brain
23	chr6:36726600-36729800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr6:36726800-36729600	Enhancers	Brain Angular Gyrus	brain
25	chr6:36726800-36729600	Enhancers	Brain Hippocampus Middle	brain
26	chr6:36726800-36729600	Enhancers	Brain Substantia Nigra	brain
27	chr6:36726800-36730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:36726800-36733800	Weak transcription	Pancreas	Pancrea
29	chr6:36727000-36730400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:36727000-36732000	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr6:36727000-36732000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr6:36727000-36732000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:36727000-36732400	Weak transcription	Fetal Muscle Leg	muscle
34	chr6:36727000-36733400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr6:36727000-36733800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:36727200-36728200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr6:36727200-36734000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr6:36727200-36736400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr6:36727400-36727600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr6:36727400-36727600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:36727400-36727600	Enhancers	Fetal Muscle Trunk	muscle
42	chr6:36727400-36735200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr6:36727400-36736200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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