Variant report

Variant	rs9324153
Chromosome Location	chr1:86158754-86158755
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:85773624..85774495-chr1:86158324..86158878,2	MCF-7	breast:
2	chr1:86048008..86048656-chr1:86158181..86159073,2	MCF-7	breast:
3	chr1:86042710..86043312-chr1:86158145..86159062,2	K562	blood:
4	chr1:86156720..86159638-chr1:86173853..86175632,2	K562	blood:
5	chr1:86046490..86052181-chr1:86153083..86160889,7	MCF-7	breast:
6	chr1:86078304..86079156-chr1:86158309..86159087,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117174	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10747324	0.81[ASN][1000 genomes]
rs10873718	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10873719	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12756841	0.81[ASN][1000 genomes]
rs1764287	0.86[ASW][hapmap]
rs1764294	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1764298	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1775987	0.86[ASW][hapmap]
rs1775993	0.84[CEU][hapmap]
rs2014733	0.86[ASW][hapmap]
rs2014750	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2026774	0.93[ASW][hapmap]
rs2389974	0.86[ASW][hapmap]
rs2389975	0.81[ASN][1000 genomes]
rs2785082	1.00[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs369999	0.81[ASN][1000 genomes]
rs381453	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs383558	0.81[ASN][1000 genomes]
rs401657	0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs420515	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs429040	0.86[ASW][hapmap]
rs430956	0.86[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs432254	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs438401	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs450953	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4949917	0.93[ASW][hapmap]
rs4949918	0.93[ASW][hapmap]
rs550329	0.85[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs6673975	0.86[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6682235	0.86[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6694808	0.93[ASW][hapmap]
rs7528385	0.86[ASN][1000 genomes]
rs7529942	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7535884	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7547023	0.86[ASW][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7554621	0.81[ASN][1000 genomes]
rs821377	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs821378	0.93[ASW][hapmap];0.84[CEU][hapmap]
rs821380	0.84[CEU][hapmap]
rs821390	0.93[ASW][hapmap];0.84[CEU][hapmap]
rs821400	0.93[ASW][hapmap]
rs821402	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs821403	0.84[CEU][hapmap]
rs821404	0.83[CEU][hapmap]
rs9324152	0.93[ASW][hapmap];0.84[CEU][hapmap]
rs9432948	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9793547	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9324153	DNASE2B	cis	cerebellum	SCAN
rs9324153	ZNHIT6	cis	cerebellum	SCAN
rs9324153	CTBS	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
2	chr1:86103600-86172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:86103600-86172600	Weak transcription	Gastric	stomach
4	chr1:86114400-86163200	Weak transcription	Esophagus	oesophagus
5	chr1:86115200-86167600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:86117000-86165800	Weak transcription	Fetal Brain Female	brain
7	chr1:86117600-86172000	Weak transcription	Small Intestine	intestine
8	chr1:86119600-86172000	Weak transcription	Colonic Mucosa	Colon
9	chr1:86119800-86171800	Weak transcription	Fetal Brain Male	brain
10	chr1:86132800-86165800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:86133600-86163400	Weak transcription	Fetal Heart	heart
12	chr1:86134200-86172600	Weak transcription	Right Ventricle	heart
13	chr1:86134600-86172400	Weak transcription	Stomach Mucosa	stomach
14	chr1:86135200-86171200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr1:86135600-86172000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:86141600-86171800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:86142400-86170600	Weak transcription	Brain Germinal Matrix	brain
18	chr1:86142600-86163800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:86142600-86166200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:86142600-86166400	Weak transcription	Lung	lung
21	chr1:86142600-86170800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:86142600-86171000	Weak transcription	Brain Substantia Nigra	brain
23	chr1:86142600-86172600	Weak transcription	Thymus	Thymus
24	chr1:86142600-86172600	Weak transcription	Spleen	Spleen
25	chr1:86142800-86166400	Weak transcription	Placenta	Placenta
26	chr1:86144200-86163600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:86144200-86165000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr1:86144200-86166200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:86144200-86166800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:86144200-86168200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr1:86144400-86165800	Weak transcription	K562	blood
32	chr1:86144400-86167600	Weak transcription	Fetal Lung	lung
33	chr1:86144400-86170400	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:86145800-86165400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:86146000-86166000	Weak transcription	Fetal Intestine Large	intestine
36	chr1:86146000-86170600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:86146200-86164200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:86146400-86165800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:86146600-86165200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:86146600-86166200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr1:86147000-86163200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr1:86147000-86172600	Weak transcription	Brain Angular Gyrus	brain
43	chr1:86147200-86169400	Weak transcription	Brain Anterior Caudate	brain
44	chr1:86147200-86172000	Weak transcription	Fetal Kidney	kidney
45	chr1:86147200-86172600	Weak transcription	Psoas Muscle	Psoas
46	chr1:86147200-86172800	Weak transcription	Aorta	Aorta
47	chr1:86147600-86166200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:86149000-86166000	Weak transcription	HepG2	liver
49	chr1:86152200-86161000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:86152600-86165400	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links