Variant report

Variant	rs9294385
Chromosome Location	chr6:88393958-88393959
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88391233..88396986-chr6:88407673..88412388,9	K562	blood:
2	chr6:88391827..88396132-chr6:88405533..88410317,6	MCF-7	breast:
3	chr6:88388879..88390685-chr6:88392735..88395490,2	MCF-7	breast:
4	chr6:88392656..88394739-chr6:88399479..88401208,2	K562	blood:
5	chr6:88388778..88396986-chr6:88407117..88413072,10	K562	blood:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1052623	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.96[ASN][1000 genomes]
rs1075665	0.86[ASN][1000 genomes]
rs11962148	0.95[JPT][hapmap]
rs12530371	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs13214442	0.94[JPT][hapmap]
rs2246051	0.84[JPT][hapmap]
rs2300904	0.94[JPT][hapmap]
rs2300908	0.95[JPT][hapmap]
rs3778671	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs3818057	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4354121	0.81[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4707385	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4707386	0.98[ASN][1000 genomes]
rs58305152	0.86[ASN][1000 genomes]
rs6454634	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs6927171	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs6928057	0.95[JPT][hapmap]
rs9294384	0.88[ASN][1000 genomes]
rs9444509	0.95[JPT][hapmap]
rs9444514	1.00[JPT][hapmap]
rs9444531	0.91[ASN][1000 genomes]
rs9444534	0.94[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9444536	0.96[ASN][1000 genomes]
rs9450716	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs9450717	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs9450740	0.85[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap]
rs9450749	0.87[ASW][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9450750	0.87[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9450751	0.85[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9450756	0.87[ASW][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs9450760	0.84[ASN][1000 genomes]
rs9450763	0.86[ASN][1000 genomes]
rs9450773	0.96[ASN][1000 genomes]
rs9474	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.96[ASN][1000 genomes]

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	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9294385	C6orf162	cis	cerebellum	SCAN
rs9294385	SLC35A1	Cis_1M	lymphoblastoid	RTeQTL
rs9294385	AKIRIN2	cis	cerebellum	SCAN
rs9294385	SLC35A1	cis	parietal	SCAN
rs9294385	C6orf162	cis	parietal	SCAN
rs9294385	SLC35A1	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
5	chr6:88349400-88397400	Weak transcription	Ovary	ovary
6	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
8	chr6:88381400-88400600	Weak transcription	Right Atrium	heart
9	chr6:88385400-88394800	Weak transcription	Brain Substantia Nigra	brain
10	chr6:88385400-88399800	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:88385400-88401200	Weak transcription	Fetal Heart	heart
12	chr6:88385800-88398600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr6:88385800-88399200	Weak transcription	Brain Anterior Caudate	brain
14	chr6:88386000-88396400	Weak transcription	Lung	lung
15	chr6:88386200-88399000	Weak transcription	Gastric	stomach
16	chr6:88387400-88398600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:88387600-88394800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr6:88387600-88397000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:88387600-88407000	Weak transcription	Fetal Kidney	kidney
20	chr6:88387800-88400600	Weak transcription	K562	blood
21	chr6:88388000-88394200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr6:88388000-88394600	Weak transcription	Fetal Muscle Leg	muscle
23	chr6:88388000-88394800	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:88388000-88397200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:88388000-88401400	Weak transcription	Placenta	Placenta
26	chr6:88388000-88410400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:88389200-88394800	Weak transcription	Thymus	Thymus
28	chr6:88389200-88406800	Weak transcription	Fetal Stomach	stomach
29	chr6:88389400-88396400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr6:88389600-88401400	Weak transcription	Fetal Brain Female	brain
31	chr6:88389800-88394400	Weak transcription	Fetal Lung	lung
32	chr6:88390200-88401200	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr6:88390400-88394200	Weak transcription	Primary T cells from cord blood	blood
34	chr6:88390400-88396000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr6:88390400-88398800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr6:88390400-88399600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:88390400-88400400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:88390400-88400800	Weak transcription	Pancreas	Pancrea
39	chr6:88390400-88401200	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:88390400-88401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:88390400-88401800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:88390400-88405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr6:88390400-88410000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:88390800-88394800	Weak transcription	Adipose Nuclei	Adipose
45	chr6:88391000-88405200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr6:88391200-88394400	Weak transcription	Fetal Intestine Small	intestine
47	chr6:88391200-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:88391400-88395000	Weak transcription	Brain Angular Gyrus	brain
49	chr6:88391400-88395400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:88391400-88400800	Weak transcription	Brain Germinal Matrix	brain

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