Variant report

Variant	rs1124590
Chromosome Location	chr11:77703983-77703984
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77530218..77533723-chr11:77703658..77708132,10	MCF-7	breast:
2	chr11:77703909..77705487-chr11:77851104..77854100,2	K562	blood:

Variant related genes	Relation type
ENSG00000087884	Chromatin interaction
ENSG00000048649	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12419883	0.91[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12420528	0.88[CEU][hapmap];0.91[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12575197	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12575337	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17135969	0.89[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs1968666	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2051484	0.89[CEU][hapmap]
rs2186564	0.89[CEU][hapmap];0.92[YRI][hapmap]
rs3740681	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758664	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3886195	0.90[CEU][hapmap];0.85[YRI][hapmap]
rs4245454	0.90[CEU][hapmap];0.85[YRI][hapmap]
rs4944176	0.89[CEU][hapmap];0.92[YRI][hapmap]
rs4944178	0.89[CEU][hapmap];0.92[YRI][hapmap]
rs4944186	0.89[AMR][1000 genomes]
rs4945223	0.90[CEU][hapmap]
rs4945227	0.83[CHB][hapmap]
rs4945229	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4945230	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57491077	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58992562	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59363412	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60124679	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60143695	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60355295	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60509203	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61201377	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61226220	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61487443	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67194469	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7107903	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72939484	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72941310	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941320	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941328	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941334	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941336	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941350	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941354	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7935050	0.93[JPT][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7946876	0.81[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.90[AMR][1000 genomes];0.85[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	nsv1050891	chr11:77416645-77788002	Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1037292	chr11:77431583-77745934	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv541092	chr11:77431583-77745934	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949316	chr11:77454076-77769885	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv520740	chr11:77553638-77997936	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
6	nsv1035753	chr11:77577384-77866386	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv541093	chr11:77577384-77866386	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1124590	RP11-91P24.6	cis	Artery Tibial	GTEx
rs1124590	RSF1	Cis_1M	lymphoblastoid	RTeQTL
rs1124590	RP11-91P24.6	cis	Thyroid	GTEx
rs1124590	AAMDC	cis	Artery Tibial	GTEx
rs1124590	INTS4	Cis_1M	lymphoblastoid	RTeQTL
rs1124590	RP11-91P24.7	cis	Thyroid	GTEx
rs1124590	AAMDC	cis	Thyroid	GTEx
rs1124590	RP11-91P24.7	cis	Artery Tibial	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77661400-77704400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr11:77664200-77704000	Weak transcription	NHEK	skin
3	chr11:77665800-77704200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr11:77666000-77704400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr11:77667600-77704200	Weak transcription	NHLF	lung
6	chr11:77671200-77704200	Weak transcription	NHDF-Ad	bronchial
7	chr11:77679000-77704200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr11:77681000-77704200	Weak transcription	HSMMtube	muscle
9	chr11:77688200-77704800	Weak transcription	Stomach Mucosa	stomach
10	chr11:77689000-77704800	Weak transcription	Fetal Heart	heart
11	chr11:77689200-77704800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr11:77690400-77704200	Weak transcription	HMEC	breast
13	chr11:77690600-77704000	Weak transcription	Brain Anterior Caudate	brain
14	chr11:77690600-77704000	Weak transcription	Brain Substantia Nigra	brain
15	chr11:77690600-77704200	Weak transcription	Gastric	stomach
16	chr11:77690600-77704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr11:77690600-77704400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:77690800-77704200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:77690800-77704200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr11:77690800-77704200	Weak transcription	Small Intestine	intestine
21	chr11:77691400-77704000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr11:77691400-77704800	Weak transcription	Colonic Mucosa	Colon
23	chr11:77692000-77704000	Weak transcription	Colon Smooth Muscle	Colon
24	chr11:77692600-77704000	Weak transcription	A549	lung
25	chr11:77692600-77704200	Weak transcription	HUVEC	blood vessel
26	chr11:77696400-77704400	Weak transcription	Fetal Kidney	kidney
27	chr11:77699000-77704000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr11:77699000-77704000	Weak transcription	Brain Germinal Matrix	brain
29	chr11:77699000-77704000	Strong transcription	Fetal Muscle Trunk	muscle
30	chr11:77700000-77704000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:77700200-77704200	Strong transcription	Fetal Stomach	stomach
32	chr11:77701200-77704200	Weak transcription	Psoas Muscle	Psoas
33	chr11:77701400-77704000	Weak transcription	Fetal Lung	lung
34	chr11:77701400-77704200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr11:77701400-77704400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr11:77701400-77704400	Weak transcription	Esophagus	oesophagus
37	chr11:77701600-77704400	Weak transcription	Ovary	ovary
38	chr11:77701600-77704400	Weak transcription	Right Ventricle	heart
39	chr11:77701600-77704800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr11:77701600-77704800	Weak transcription	Lung	lung
41	chr11:77701800-77704000	Weak transcription	HepG2	liver
42	chr11:77701800-77704200	Weak transcription	Left Ventricle	heart
43	chr11:77701800-77704800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr11:77702000-77704400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr11:77702200-77704000	Weak transcription	Brain Angular Gyrus	brain
46	chr11:77702200-77704000	Genic enhancers	Dnd41	blood
47	chr11:77702200-77704200	Weak transcription	Brain Cingulate Gyrus	brain
48	chr11:77702200-77704200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr11:77702200-77704200	Weak transcription	HSMM	muscle
50	chr11:77702200-77704400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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