Variant report

Variant	rs1561328
Chromosome Location	chr2:86272758-86272759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:86076023..86078955-chr2:86270919..86273082,2	MCF-7	breast:
2	chr2:86271666..86274392-chr2:86276622..86278866,2	MCF-7	breast:
3	chr2:86271262..86274058-chr2:86286293..86288618,2	K562	blood:
4	chr2:86270899..86273641-chr2:86288128..86290154,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115525	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10165327	0.86[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs10168635	0.86[ASN][1000 genomes]
rs10174095	1.00[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10179090	0.86[ASN][1000 genomes]
rs1019591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1036554	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10427394	0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs11884765	0.92[GIH][hapmap]
rs11899576	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12612513	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12614260	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12617717	0.87[EUR][1000 genomes]
rs12620810	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs12621992	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12622009	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12622715	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs12624126	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13384563	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13390702	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1559516	0.86[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs17026701	1.00[CEU][hapmap]
rs17026729	1.00[CEU][hapmap]
rs17026854	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17026940	0.92[GIH][hapmap]
rs17027011	0.86[ASN][1000 genomes]
rs17584578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17618001	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2018608	0.87[EUR][1000 genomes]
rs2118521	0.80[EUR][1000 genomes]
rs2164879	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2228352	0.92[GIH][hapmap]
rs2241435	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2241437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2278085	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2278087	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2278088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288121	0.85[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs2289237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[ASN][1000 genomes]
rs2303339	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2303340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs311562	0.87[ASN][1000 genomes]
rs311566	0.87[ASN][1000 genomes]
rs311567	0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs34522092	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3731819	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770066	0.86[ASN][1000 genomes]
rs3770081	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770087	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3770089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3770090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3810827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815840	0.87[ASN][1000 genomes]
rs4832242	0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs4832250	0.86[CHB][hapmap];0.83[CHD][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs56104203	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56326127	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56977454	0.90[ASN][1000 genomes]
rs57083584	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57398459	0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58186343	0.92[ASN][1000 genomes]
rs58365138	0.90[ASN][1000 genomes]
rs58898686	0.92[ASN][1000 genomes]
rs59835600	0.88[ASN][1000 genomes]
rs59891296	0.99[AFR][1000 genomes]
rs60649958	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6750765	0.95[ASN][1000 genomes]
rs73943946	0.95[ASN][1000 genomes]
rs73947314	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7562837	0.81[AMR][1000 genomes]
rs7608262	0.94[ASN][1000 genomes]
rs918857	0.94[AFR][1000 genomes]
rs918858	0.92[AFR][1000 genomes]
rs9789563	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973880	0.80[EUR][1000 genomes];0.86[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	esv2751903	chr2:86253542-86505453	Active TSS Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv531380	chr2:86253552-86469217	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv870120	chr2:86265437-86343058	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1561328	C2orf23	cis	multi-tissue	Pritchard
rs1561328	LOC90784	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86251200-86273200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:86251200-86281400	Strong transcription	H9 Cell Line	embryonic stem cell
3	chr2:86251200-86283000	Strong transcription	HepG2	liver
4	chr2:86251200-86283200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:86251200-86285000	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr2:86251200-86285200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:86252000-86331200	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:86252200-86282600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr2:86252200-86285200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:86252400-86283200	Strong transcription	H1 Cell Line	embryonic stem cell
11	chr2:86252600-86276800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:86264000-86281800	Strong transcription	Fetal Brain Female	brain
13	chr2:86264000-86332000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:86264200-86275400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:86264400-86279400	Strong transcription	Hela-S3	cervix
16	chr2:86264400-86285400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr2:86264400-86285400	Strong transcription	A549	lung
18	chr2:86264600-86273800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:86264800-86273000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr2:86264800-86275400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:86265200-86281600	Strong transcription	HMEC	breast
22	chr2:86265200-86284000	Strong transcription	NHEK	skin
23	chr2:86265200-86330000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:86265400-86282600	Strong transcription	Esophagus	oesophagus
25	chr2:86265400-86285200	Strong transcription	Fetal Intestine Large	intestine
26	chr2:86265400-86289800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:86265400-86289800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:86265600-86273200	Strong transcription	Aorta	Aorta
29	chr2:86265600-86274600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:86265600-86282000	Strong transcription	K562	blood
31	chr2:86265600-86282400	Strong transcription	Brain Germinal Matrix	brain
32	chr2:86265600-86289800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:86265800-86274400	Strong transcription	Brain Anterior Caudate	brain
34	chr2:86265800-86276600	Strong transcription	Brain Cingulate Gyrus	brain
35	chr2:86265800-86278600	Weak transcription	Small Intestine	intestine
36	chr2:86265800-86280400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:86265800-86284000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:86265800-86305400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:86266000-86273000	Strong transcription	Colonic Mucosa	Colon
40	chr2:86266000-86274600	Strong transcription	Brain Angular Gyrus	brain
41	chr2:86266000-86275200	Strong transcription	Colon Smooth Muscle	Colon
42	chr2:86266000-86276600	Strong transcription	Brain Hippocampus Middle	brain
43	chr2:86266000-86278000	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr2:86266000-86281800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:86266000-86282600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr2:86266000-86282800	Strong transcription	Gastric	stomach
47	chr2:86266000-86282800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr2:86266000-86283800	Strong transcription	Fetal Intestine Small	intestine
49	chr2:86266000-86287800	Weak transcription	Right Atrium	heart
50	chr2:86266200-86280600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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