Variant report

Variant	rs11173124
Chromosome Location	chr12:60119929-60119930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49658530..49660065-chr12:60117351..60120020,2	MCF-7	breast:
2	chr12:60118954..60121545-chr2:160471632..160473698,2	MCF-7	breast:
3	chr12:60118809..60120952-chr12:60126355..60129129,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224152	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000123636	Chromatin interaction
ENSG00000167553	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10506399	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11173126	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11173133	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11173134	0.89[ASN][1000 genomes]
rs11173137	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11173158	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11173159	0.82[EUR][1000 genomes]
rs12227214	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12231311	0.90[ASN][1000 genomes]
rs12231693	0.89[ASN][1000 genomes]
rs12232002	0.89[ASN][1000 genomes]
rs12812799	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17572877	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17572912	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17649424	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17650311	0.86[ASN][1000 genomes]
rs1795884	0.82[ASN][1000 genomes]
rs1795896	0.81[ASN][1000 genomes]
rs2365317	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2365318	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2706295	0.81[ASN][1000 genomes]
rs2706306	0.81[ASN][1000 genomes]
rs2706309	0.82[ASN][1000 genomes]
rs2706319	0.82[ASN][1000 genomes]
rs2711655	0.81[ASN][1000 genomes]
rs2711656	0.81[ASN][1000 genomes]
rs2711659	0.81[ASN][1000 genomes]
rs2711668	0.81[ASN][1000 genomes]
rs2711670	0.82[ASN][1000 genomes]
rs2711672	0.82[ASN][1000 genomes]
rs2711677	0.82[ASN][1000 genomes]
rs2711691	0.81[ASN][1000 genomes]
rs34264510	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34639075	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34785387	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35365387	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35518979	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3763980	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4583011	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56682442	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61174819	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581274	0.87[EUR][1000 genomes]
rs66802005	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs66861118	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68028492	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7133415	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7303876	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7978598	0.81[ASN][1000 genomes]
rs7979504	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9705733	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9788077	0.85[AMR][1000 genomes];0.87[EUR][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	nsv869425	chr12:59746898-60479741	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv899131	chr12:59942122-60124089	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv3365928	chr12:60042531-60343212	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv899132	chr12:60087572-60211476	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11173124	RP11-813P10.2	cis	Whole Blood	GTEx
rs11173124	SLC16A7	Cis_1M	lymphoblastoid	RTeQTL
rs11173124	RP11-813P10.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:60069600-60131400	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:60089400-60126000	Weak transcription	Left Ventricle	heart
3	chr12:60093800-60126600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr12:60094000-60127200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr12:60094200-60127200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:60099200-60126600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:60099400-60130400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:60099600-60143200	Weak transcription	Primary B cells from peripheral blood	blood
9	chr12:60100000-60175200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:60100400-60126400	Weak transcription	Primary B cells from cord blood	blood
11	chr12:60100600-60127200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:60101800-60122000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:60104200-60138000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr12:60105600-60129200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:60109400-60121800	Weak transcription	Right Ventricle	heart
16	chr12:60109400-60126600	Weak transcription	Primary T cells from cord blood	blood
17	chr12:60110200-60141400	Weak transcription	Dnd41	blood
18	chr12:60112600-60126800	Weak transcription	Adipose Nuclei	Adipose
19	chr12:60113000-60143600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr12:60117400-60120600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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