Variant report

Variant	rs12420357
Chromosome Location	chr11:73396061-73396062
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	chr11:73375007..73377512-chr11:73395012..73396634,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000252732	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10793065	0.85[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes]
rs10793066	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898930	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10898935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898936	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898938	0.87[TSI][hapmap];0.94[YRI][hapmap]
rs11235861	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11235862	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11235876	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];0.98[TSI][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11235883	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11235884	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11602887	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12788229	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12788426	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1404976	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1525749	0.85[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap]
rs1614987	0.82[EUR][1000 genomes]
rs1632159	0.89[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap]
rs1670537	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs1670543	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs1670557	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1670564	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1670565	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1723843	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[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];0.94[YRI][hapmap]
rs1723848	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1792156	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap]
rs1792160	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1792165	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1792166	0.82[EUR][1000 genomes]
rs1792174	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.80[EUR][1000 genomes]
rs1792193	0.86[CHB][hapmap];0.84[CHD][hapmap]
rs1792198	0.92[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap]
rs2008734	0.85[CEU][hapmap]
rs2140893	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];0.94[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2367187	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2367188	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511261	0.82[EUR][1000 genomes]
rs2886816	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3817514	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs3862797	0.84[CEU][hapmap];0.82[JPT][hapmap]
rs7104603	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119055	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];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925514	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7933372	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7938731	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs868667	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];0.94[YRI][hapmap];0.83[EUR][1000 genomes]
rs9705336	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv530624	chr11:73114283-73646329	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv492091	chr11:73285970-73844424	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS 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	85 gene(s)	inside rSNPs	diseases
4	nsv1045149	chr11:73314565-73581908	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv530641	chr11:73358393-73638725	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv390	chr11:73388188-73432899	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv19003	chr11:73394993-73398426	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12420357	MRPL48	cis	multi-tissue	Pritchard
rs12420357	PAAF1	cis	lymphoblastoid	seeQTL
rs12420357	RNF121	cis	cerebellum	SCAN
rs12420357	MRPL48	Cis_1M	lymphoblastoid	RTeQTL
rs12420357	MRPL48	cis	cerebellum	SCAN
rs12420357	MRPL48	cis	lymphoblastoid	seeQTL
rs12420357	PLEKHB1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73374400-73427200	Weak transcription	A549	lung
2	chr11:73375200-73404400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:73375800-73400000	Weak transcription	Lung	lung
4	chr11:73375800-73416200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr11:73376200-73398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:73376600-73399200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:73376600-73400000	Weak transcription	Spleen	Spleen
8	chr11:73377000-73400000	Weak transcription	Psoas Muscle	Psoas
9	chr11:73381800-73400000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr11:73382200-73399000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr11:73382200-73436000	Weak transcription	Small Intestine	intestine
12	chr11:73382200-73441200	Weak transcription	Stomach Mucosa	stomach
13	chr11:73382400-73421600	Weak transcription	Gastric	stomach
14	chr11:73382800-73400400	Weak transcription	Pancreas	Pancrea
15	chr11:73383200-73399000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:73383400-73427200	Weak transcription	Fetal Heart	heart
17	chr11:73384000-73427600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr11:73384800-73401800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr11:73385000-73449800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr11:73385600-73398800	Weak transcription	Aorta	Aorta
21	chr11:73385800-73411400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:73386400-73397800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr11:73386600-73399400	Weak transcription	Esophagus	oesophagus
24	chr11:73386800-73399400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr11:73387400-73410800	Weak transcription	Colonic Mucosa	Colon
26	chr11:73388200-73396200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr11:73388200-73396600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:73388400-73396200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr11:73388400-73398000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:73389000-73399400	Weak transcription	Left Ventricle	heart
31	chr11:73389000-73445400	Weak transcription	Fetal Brain Male	brain
32	chr11:73389200-73397200	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:73389200-73398800	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr11:73389200-73400200	Weak transcription	Fetal Kidney	kidney
35	chr11:73389200-73400800	Strong transcription	Fetal Intestine Small	intestine
36	chr11:73389200-73404800	Weak transcription	K562	blood
37	chr11:73389200-73410600	Weak transcription	Brain Angular Gyrus	brain
38	chr11:73389200-73416800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:73389200-73427400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:73389200-73440200	Weak transcription	Right Ventricle	heart
41	chr11:73389400-73398600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr11:73389400-73399000	Weak transcription	Colon Smooth Muscle	Colon
43	chr11:73389400-73404800	Weak transcription	Brain Substantia Nigra	brain
44	chr11:73389600-73400400	Weak transcription	GM12878-XiMat	blood
45	chr11:73390200-73399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:73390600-73397000	Weak transcription	Brain Hippocampus Middle	brain
47	chr11:73390600-73398400	Weak transcription	HepG2	liver
48	chr11:73390600-73399200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr11:73390800-73397200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:73390800-73399000	Weak transcription	NH-A	brain

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