Variant report

Variant	rs9356943
Chromosome Location	chr6:24709830-24709831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24709253..24711356-chr6:24713475..24715005,2	MCF-7	breast:
2	chr6:24703121..24705782-chr6:24707406..24711144,3	MCF-7	breast:
3	chr6:24697429..24699456-chr6:24708438..24711427,3	K562	blood:
4	chr6:24707645..24711659-chr6:24779375..24784848,6	K562	blood:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11753290	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs17249505	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1923187	0.93[CEU][hapmap]
rs3181228	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4544900	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56344861	0.90[EUR][1000 genomes]
rs6909099	0.83[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes]
rs6917209	0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6927947	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6928668	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6931809	0.83[CEU][hapmap];0.96[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs6937327	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6937533	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7757919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7765904	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9358791	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9358793	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9366580	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9379685	0.87[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3508002	chr6:24618580-24732946	Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv3508003	chr6:24618580-24732946	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv515732	chr6:24705835-24709830	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9356943	C6orf62	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24696600-24710400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr6:24697800-24715800	Strong transcription	Fetal Thymus	thymus
3	chr6:24698000-24711600	Strong transcription	Primary T cells from cord blood	blood
4	chr6:24698200-24716200	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr6:24698200-24716200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:24698200-24716400	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:24698200-24717400	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:24698400-24717400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr6:24698600-24715200	Weak transcription	Fetal Heart	heart
10	chr6:24698600-24716200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:24698600-24716200	Weak transcription	Right Atrium	heart
12	chr6:24699000-24716600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:24699000-24717400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:24699600-24712800	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr6:24699800-24712400	Strong transcription	Dnd41	blood
16	chr6:24700000-24716800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:24700200-24713200	Weak transcription	Stomach Mucosa	stomach
18	chr6:24700600-24712400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr6:24701000-24711400	Strong transcription	Brain Hippocampus Middle	brain
20	chr6:24701200-24710600	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr6:24701200-24711400	Strong transcription	Liver	Liver
22	chr6:24701200-24712200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:24701200-24713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr6:24701200-24714200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:24701400-24711000	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:24701400-24711400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:24701400-24712200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr6:24701400-24713000	Strong transcription	Primary B cells from cord blood	blood
29	chr6:24701400-24713000	Strong transcription	Primary hematopoietic stem cells	blood
30	chr6:24701400-24713200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:24701400-24713200	Strong transcription	Fetal Intestine Large	intestine
32	chr6:24701400-24715400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr6:24701400-24716800	Strong transcription	Placenta	Placenta
34	chr6:24701600-24712000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr6:24701600-24712400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:24701600-24714800	Strong transcription	HUVEC	blood vessel
37	chr6:24701600-24716200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr6:24701600-24716200	Strong transcription	Stomach Smooth Muscle	stomach
39	chr6:24701600-24716200	Strong transcription	HMEC	breast
40	chr6:24701600-24716600	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:24701600-24716600	Strong transcription	Fetal Muscle Leg	muscle
42	chr6:24701800-24715400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:24701800-24715600	Strong transcription	Osteobl	bone
44	chr6:24701800-24716200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:24701800-24716800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:24702000-24710800	Strong transcription	Fetal Brain Female	brain
47	chr6:24702000-24712000	Strong transcription	NHEK	skin
48	chr6:24702200-24711000	Strong transcription	Brain Anterior Caudate	brain
49	chr6:24702200-24711200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr6:24702200-24711400	Strong transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links