Variant report

Variant	rs853235
Chromosome Location	chr12:51375969-51375970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51375354..51377058-chr12:51377116..51379193,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1005559	0.82[JPT][hapmap]
rs1048230	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs10506298	0.81[ASN][1000 genomes]
rs10506299	0.81[ASN][1000 genomes]
rs11169642	0.88[JPT][hapmap]
rs11169648	0.81[ASN][1000 genomes]
rs11169649	0.81[ASN][1000 genomes]
rs11169652	0.81[ASN][1000 genomes]
rs11169654	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs11169655	0.81[ASN][1000 genomes]
rs11519977	0.81[ASN][1000 genomes]
rs12366756	0.81[JPT][hapmap]
rs12369639	0.86[JPT][hapmap]
rs12810659	0.81[ASN][1000 genomes]
rs12817386	0.81[ASN][1000 genomes]
rs12824958	0.82[JPT][hapmap]
rs12830048	0.81[ASN][1000 genomes]
rs15897	0.81[ASN][1000 genomes]
rs17125137	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs224565	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs224577	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs224589	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs224591	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2285228	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2285230	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301529	0.82[JPT][hapmap]
rs2516742	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2630364	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs319932	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs407135	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs422637	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs422982	0.95[CEU][hapmap];0.91[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs440595	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4471501	0.95[CEU][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs454520	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs67259551	0.81[ASN][1000 genomes]
rs706801	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs706802	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7488909	0.94[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs829022	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[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	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	esv34039	chr12:51326702-51671911	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
3	nsv1053466	chr12:51350285-51375969	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs853235	SLC48A1	cis	cerebellum	SCAN
rs853235	MCRS1	cis	parietal	SCAN
rs853235	DDN	cis	cerebellum	SCAN
rs853235	TFCP2	cis	cerebellum	SCAN
rs853235	LETMD1	Cis_1M	lymphoblastoid	RTeQTL
rs853235	CSRNP2	cis	cerebellum	SCAN
rs853235	SLC11A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51323000-51377200	Weak transcription	Aorta	Aorta
2	chr12:51328800-51378000	Weak transcription	Brain Substantia Nigra	brain
3	chr12:51331400-51378400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:51331800-51382000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:51331800-51382000	Weak transcription	Ovary	ovary
6	chr12:51341600-51378200	Weak transcription	Right Ventricle	heart
7	chr12:51341800-51383200	Weak transcription	Fetal Brain Male	brain
8	chr12:51342800-51378400	Weak transcription	NHLF	lung
9	chr12:51344000-51382000	Weak transcription	Esophagus	oesophagus
10	chr12:51344600-51381600	Weak transcription	Spleen	Spleen
11	chr12:51347200-51378000	Weak transcription	Brain Angular Gyrus	brain
12	chr12:51347400-51378000	Weak transcription	Brain Anterior Caudate	brain
13	chr12:51350800-51380600	Weak transcription	Fetal Lung	lung
14	chr12:51354400-51383800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr12:51355600-51378000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:51355800-51378000	Weak transcription	A549	lung
17	chr12:51357600-51378000	Weak transcription	Psoas Muscle	Psoas
18	chr12:51358800-51377800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr12:51359800-51380400	Weak transcription	Fetal Kidney	kidney
20	chr12:51360200-51381800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:51360600-51381000	Weak transcription	Primary B cells from cord blood	blood
22	chr12:51360600-51381800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:51361600-51382200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr12:51362400-51376800	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:51362400-51378600	Weak transcription	NH-A	brain
26	chr12:51362400-51382000	Weak transcription	Lung	lung
27	chr12:51362600-51378000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:51362800-51384400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr12:51363400-51384000	Weak transcription	Colonic Mucosa	Colon
30	chr12:51363600-51381200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:51364000-51380400	Weak transcription	K562	blood
32	chr12:51364600-51378400	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:51364600-51384400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:51366000-51377800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr12:51366000-51378000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr12:51366000-51378400	Weak transcription	HSMMtube	muscle
37	chr12:51366000-51378600	Weak transcription	HSMM	muscle
38	chr12:51366200-51380000	Weak transcription	Dnd41	blood
39	chr12:51366400-51377800	Weak transcription	NHDF-Ad	bronchial
40	chr12:51366400-51378400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:51366400-51379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:51366600-51378000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr12:51366600-51380200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr12:51366800-51378400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr12:51366800-51378600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr12:51366800-51382000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:51367000-51379600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr12:51367000-51380400	Weak transcription	Fetal Brain Female	brain
49	chr12:51367000-51380400	Weak transcription	Fetal Muscle Leg	muscle
50	chr12:51367000-51382000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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