Variant report

Variant	rs7867856
Chromosome Location	chr9:97671376-97671377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97580281..97582910-chr9:97669782..97672711,3	MCF-7	breast:
2	chr9:97621787..97623596-chr9:97671086..97673869,2	MCF-7	breast:
3	chr9:97670511..97672510-chr9:97682637..97684241,2	K562	blood:
4	chr9:97666485..97669668-chr9:97669881..97673620,4	MCF-7	breast:
5	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
6	chr9:97670509..97672235-chr9:97673084..97674732,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230815	Chromatin interaction
ENSG00000148120	Chromatin interaction
ENSG00000252153	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10125566	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1020962	1.00[CEU][hapmap]
rs10217441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1038092	1.00[ASW][hapmap];1.00[CEU][hapmap]
rs10732407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10733756	0.82[EUR][1000 genomes]
rs10739988	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10739990	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10739991	0.85[EUR][1000 genomes]
rs10761362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10761363	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761371	1.00[CEU][hapmap]
rs10821411	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993386	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10993471	1.00[ASW][hapmap]
rs1113967	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12554043	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs12554454	0.84[ASN][1000 genomes]
rs12555128	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes]
rs1382411	0.84[ASN][1000 genomes]
rs1382412	0.84[ASN][1000 genomes]
rs1530331	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs1542107	0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1542108	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1564235	1.00[CEU][hapmap]
rs1571896	1.00[CEU][hapmap]
rs16911862	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1871220	1.00[CEU][hapmap]
rs1888944	1.00[CEU][hapmap]
rs191654	0.85[EUR][1000 genomes]
rs2026399	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2061798	1.00[CEU][hapmap]
rs2061799	1.00[CEU][hapmap]
rs2061801	1.00[CEU][hapmap]
rs2095069	0.88[MEX][hapmap];1.00[TSI][hapmap]
rs2099868	0.85[EUR][1000 genomes]
rs2104888	0.81[AMR][1000 genomes]
rs2119953	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2165715	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2406897	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2406898	1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2584805	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs2897523	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35322834	0.81[AMR][1000 genomes]
rs356125	1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs356128	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs356132	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs356133	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs356136	0.85[EUR][1000 genomes]
rs356139	0.85[EUR][1000 genomes]
rs356145	0.85[EUR][1000 genomes]
rs356147	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs356148	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs356149	0.85[EUR][1000 genomes]
rs365465	0.85[EUR][1000 genomes]
rs367319	0.85[EUR][1000 genomes]
rs3739748	1.00[CEU][hapmap]
rs3847311	0.85[EUR][1000 genomes]
rs3886568	0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3887267	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs3910730	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs438742	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs448899	0.85[EUR][1000 genomes]
rs456276	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs457795	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs4743968	0.85[EUR][1000 genomes]
rs4743972	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743973	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743975	1.00[CEU][hapmap]
rs4743977	1.00[CEU][hapmap]
rs4744382	0.85[EUR][1000 genomes]
rs4744388	0.85[EUR][1000 genomes]
rs4744389	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4744402	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4744421	1.00[CEU][hapmap]
rs555799	0.82[EUR][1000 genomes]
rs562605	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs60120	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs6479569	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs6479574	1.00[CHB][hapmap]
rs6479575	0.85[EUR][1000 genomes]
rs6479578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479579	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6479581	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6479582	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479583	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66642068	0.84[ASN][1000 genomes]
rs67208365	0.85[EUR][1000 genomes]
rs68090960	0.85[EUR][1000 genomes]
rs7019602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7022963	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7023719	1.00[CEU][hapmap]
rs7025100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029570	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7035166	0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7038891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs7044371	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7047478	0.85[EUR][1000 genomes]
rs72748596	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72750335	0.81[AMR][1000 genomes]
rs7341710	0.85[EUR][1000 genomes]
rs7852844	0.82[EUR][1000 genomes]
rs7855781	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7864389	0.93[EUR][1000 genomes]
rs7869736	1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs894425	1.00[CHB][hapmap]
rs894426	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs894427	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9409805	0.85[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933919	chr9:97619512-97919344	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	293 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7867856	APCDD1	trans	brain	seeQTL

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97633400-97671800	Weak transcription	Esophagus	oesophagus
2	chr9:97660800-97702400	Weak transcription	Primary B cells from cord blood	blood
3	chr9:97661600-97686200	Weak transcription	Primary T cells from cord blood	blood
4	chr9:97662400-97678600	Enhancers	Brain Substantia Nigra	brain
5	chr9:97662600-97680400	Enhancers	Brain Hippocampus Middle	brain
6	chr9:97664800-97671800	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:97664800-97672000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:97664800-97672200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:97664800-97673400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:97664800-97673400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:97664800-97674200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr9:97665200-97674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:97665400-97674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr9:97666000-97672000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:97666000-97678600	Enhancers	Brain Cingulate Gyrus	brain
16	chr9:97666600-97674400	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:97667400-97674600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:97667800-97675200	Enhancers	Brain Anterior Caudate	brain
19	chr9:97668000-97672800	Weak transcription	Brain Germinal Matrix	brain
20	chr9:97668800-97672000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr9:97669000-97671600	Enhancers	Fetal Muscle Leg	muscle
22	chr9:97669000-97673000	Enhancers	Stomach Mucosa	stomach
23	chr9:97669000-97673600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr9:97669000-97675200	Enhancers	Fetal Lung	lung
25	chr9:97669000-97678200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:97669200-97672400	Weak transcription	Spleen	Spleen
27	chr9:97669200-97678400	Enhancers	Fetal Heart	heart
28	chr9:97669600-97673000	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr9:97669800-97671600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr9:97669800-97678200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr9:97670000-97671400	Enhancers	Rectal Smooth Muscle	rectum
32	chr9:97670000-97672000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr9:97670000-97672000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:97670000-97672400	Weak transcription	Gastric	stomach
35	chr9:97670000-97678600	Weak transcription	Fetal Thymus	thymus
36	chr9:97670200-97671400	Enhancers	HSMMtube	muscle
37	chr9:97670200-97672200	Enhancers	NH-A	brain
38	chr9:97670200-97674800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:97670400-97671400	Flanking Active TSS	A549	lung
40	chr9:97670400-97672600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:97670400-97674800	Weak transcription	HUVEC	blood vessel
42	chr9:97670600-97671600	Enhancers	Fetal Intestine Small	intestine
43	chr9:97670600-97671800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr9:97670600-97671800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr9:97670600-97671800	Weak transcription	Aorta	Aorta
46	chr9:97670600-97672400	Weak transcription	Lung	lung
47	chr9:97670600-97674600	Weak transcription	Left Ventricle	heart
48	chr9:97670600-97676400	Weak transcription	Right Ventricle	heart
49	chr9:97670600-97766000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr9:97670800-97671400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links