Variant report

Variant	rs236350
Chromosome Location	chr6:36819546-36819547
allele	C/T
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:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:18 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36818424..36822217-chr6:36952499..36954853,3	K562	blood:
2	chr6:36815130..36818530-chr6:36818954..36823604,5	K562	blood:
3	chr6:36818402..36820845-chr6:36839633..36841729,2	K562	blood:
4	chr6:36819191..36821393-chr6:36826640..36829329,2	MCF-7	breast:
5	chr6:36792882..36794850-chr6:36817375..36819702,2	MCF-7	breast:
6	chr6:36811312..36813099-chr6:36818892..36821190,2	MCF-7	breast:
7	chr6:36819209..36822564-chr6:36824095..36826600,3	K562	blood:
8	chr6:36742135..36744958-chr6:36819478..36821110,2	K562	blood:
9	chr6:36794960..36797017-chr6:36818260..36820420,2	MCF-7	breast:
10	chr6:36818579..36822639-chr6:36835896..36837920,3	K562	blood:
11	chr6:36818002..36820596-chr6:36841531..36843370,2	K562	blood:
12	chr6:36799628..36801268-chr6:36817100..36819975,2	K562	blood:
13	chr6:36803679..36805737-chr6:36818259..36820032,3	K562	blood:
14	chr6:36817709..36820546-chr6:36830678..36833403,3	MCF-7	breast:
15	chr6:36778233..36779348-chr6:36818667..36819792,5	MCF-7	breast:
16	chr6:36733614..36734738-chr6:36818383..36819576,11	MCF-7	breast:
17	chr6:36816600..36820003-chr6:36855117..36857436,3	K562	blood:
18	chr6:36818907..36820999-chr6:36822300..36824076,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000137168	Chromatin interaction
ENSG00000137409	Chromatin interaction
ENSG00000198663	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs236346	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236348	1.00[CEU][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236351	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912602	0.84[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv5262	chr6:36799329-36826210	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1030015	chr6:36818510-37104446	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs236350	SCUBE3	cis	cerebellum	SCAN
rs236350	LRFN2	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36809000-36820200	Weak transcription	Thymus	Thymus
2	chr6:36809000-36823000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:36811400-36823200	Weak transcription	Esophagus	oesophagus
4	chr6:36813200-36821200	Weak transcription	Brain Hippocampus Middle	brain
5	chr6:36813200-36823200	Weak transcription	Brain Substantia Nigra	brain
6	chr6:36815400-36819800	Enhancers	Fetal Muscle Leg	muscle
7	chr6:36815600-36819800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:36816000-36819800	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr6:36816600-36823000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:36816800-36821800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr6:36817000-36819800	Enhancers	Brain Anterior Caudate	brain
12	chr6:36817000-36819800	Weak transcription	HepG2	liver
13	chr6:36817000-36820000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:36817000-36821400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:36817000-36823200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:36817000-36826200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:36817000-36841400	Weak transcription	Colonic Mucosa	Colon
18	chr6:36817200-36819600	Weak transcription	Primary T cells from cord blood	blood
19	chr6:36817200-36820000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:36817200-36820400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:36817200-36820400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:36817200-36820600	Weak transcription	Brain Germinal Matrix	brain
23	chr6:36817200-36821200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr6:36817200-36823200	Weak transcription	Gastric	stomach
25	chr6:36817200-36823200	Weak transcription	Pancreas	Pancrea
26	chr6:36817200-36823600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr6:36817200-36830200	Weak transcription	Fetal Lung	lung
28	chr6:36817200-36833400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr6:36817200-36841200	Weak transcription	Fetal Brain Male	brain
30	chr6:36817200-36842000	Weak transcription	Stomach Mucosa	stomach
31	chr6:36817400-36820800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr6:36817400-36821400	Enhancers	Fetal Heart	heart
33	chr6:36817600-36820400	Weak transcription	NHEK	skin
34	chr6:36817600-36821000	Weak transcription	Fetal Intestine Large	intestine
35	chr6:36817600-36821200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:36817600-36822400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:36817800-36820000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:36817800-36820200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:36818000-36820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:36818000-36821400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:36818000-36821400	Enhancers	Left Ventricle	heart
42	chr6:36818000-36822800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr6:36818000-36824800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
44	chr6:36818200-36819600	Weak transcription	Right Ventricle	heart
45	chr6:36818200-36820200	Weak transcription	Primary B cells from cord blood	blood
46	chr6:36818200-36820400	Weak transcription	HMEC	breast
47	chr6:36818200-36820400	Weak transcription	HUVEC	blood vessel
48	chr6:36818200-36822200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr6:36818400-36819800	Enhancers	Fetal Stomach	stomach
50	chr6:36818400-36820000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links