Variant report

Variant	rs12909161
Chromosome Location	chr15:52420491-52420492
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52418771..52421599-chr15:52429472..52431548,2	MCF-7	breast:
2	chr15:52419540..52421651-chr15:52430986..52433153,2	K562	blood:
3	chr15:52419606..52421639-chr15:52426759..52428564,2	K562	blood:
4	chr15:52419540..52421866-chr15:52430986..52433153,3	K562	blood:
5	chr15:52418174..52420901-chr15:52470720..52473128,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259709	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11070882	0.87[ASN][1000 genomes]
rs11855672	0.80[MEX][hapmap]
rs11856177	0.87[ASN][1000 genomes]
rs12438169	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12438190	0.86[EUR][1000 genomes]
rs12438194	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12438743	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12438937	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs12440956	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12593041	1.00[CEU][hapmap];0.96[GIH][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs12594679	0.86[ASN][1000 genomes]
rs12595160	0.84[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs12899030	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs12899343	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs12901354	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12901730	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12901891	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12902073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12902522	1.00[CEU][hapmap]
rs12903769	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12904831	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904889	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908742	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12908833	0.87[ASN][1000 genomes]
rs12909184	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[YRI][hapmap]
rs12909880	0.80[AMR][1000 genomes]
rs12910398	1.00[YRI][hapmap]
rs12912428	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12916557	0.87[ASN][1000 genomes]
rs2227308	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2398	0.82[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2414130	0.89[GIH][hapmap]
rs2414132	0.93[GIH][hapmap]
rs34283892	0.86[ASN][1000 genomes]
rs35709612	0.84[EUR][1000 genomes]
rs35827106	0.87[ASN][1000 genomes]
rs3794540	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3794543	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4238384	0.81[GIH][hapmap]
rs4636859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4638520	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4774608	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4776003	0.85[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4776007	0.91[CEU][hapmap]
rs4776010	0.80[MEX][hapmap]
rs62014721	0.85[EUR][1000 genomes]
rs62014722	0.84[EUR][1000 genomes]
rs7164508	1.00[YRI][hapmap]
rs7177248	0.82[CHB][hapmap]
rs8034097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS 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 target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12909161	ARPP19	cis	parietal	SCAN
rs12909161	GNB5	Cis_1M	lymphoblastoid	RTeQTL
rs12909161	KIAA1370	cis	parietal	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52404800-52428000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:52405000-52421800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr15:52405000-52427400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:52405000-52427800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr15:52405000-52428800	Weak transcription	Fetal Heart	heart
6	chr15:52405400-52426000	Weak transcription	Spleen	Spleen
7	chr15:52406400-52427800	Weak transcription	Fetal Brain Male	brain
8	chr15:52407400-52427600	Weak transcription	HSMMtube	muscle
9	chr15:52407600-52441600	Weak transcription	Fetal Lung	lung
10	chr15:52407800-52428800	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:52407800-52440400	Weak transcription	Brain Substantia Nigra	brain
12	chr15:52408200-52425800	Weak transcription	Small Intestine	intestine
13	chr15:52408600-52425600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:52408800-52428000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:52409000-52423400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:52409000-52426800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr15:52409800-52425400	Weak transcription	Fetal Intestine Small	intestine
18	chr15:52410000-52424000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:52410000-52428600	Weak transcription	Hela-S3	cervix
20	chr15:52410200-52424800	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:52410200-52441600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:52410600-52427800	Weak transcription	Adipose Nuclei	Adipose
23	chr15:52410600-52441400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr15:52411000-52425800	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr15:52411200-52428600	Weak transcription	Left Ventricle	heart
26	chr15:52412000-52427200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr15:52412000-52427800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:52412000-52441200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:52412200-52436000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr15:52412400-52421800	Weak transcription	Fetal Thymus	thymus
31	chr15:52412400-52424200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:52412400-52424200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr15:52413600-52423800	Weak transcription	Liver	Liver
34	chr15:52413600-52424200	Weak transcription	Fetal Brain Female	brain
35	chr15:52413600-52431800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:52413800-52428400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr15:52414200-52427800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr15:52414400-52428400	Weak transcription	Colon Smooth Muscle	Colon
39	chr15:52415000-52424400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr15:52416000-52427800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:52416000-52432800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr15:52416200-52431600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:52416800-52426800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:52417000-52424200	Weak transcription	Esophagus	oesophagus
45	chr15:52417000-52425800	Weak transcription	A549	lung
46	chr15:52417000-52427600	Weak transcription	HSMM	muscle
47	chr15:52417000-52436000	Weak transcription	Lung	lung
48	chr15:52417200-52424200	Weak transcription	Osteobl	bone
49	chr15:52417200-52428600	Weak transcription	NHLF	lung
50	chr15:52417200-52428800	Weak transcription	Gastric	stomach

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