Variant report

Variant	rs12417115
Chromosome Location	chr11:77526474-77526475
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr11:77525826-77526857	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77521920..77524304-chr11:77525173..77528253,3	MCF-7	breast:
2	chr11:77523579..77527566-chr11:77528400..77532529,6	K562	blood:

Variant related genes	Relation type
ENSG00000219529	TF binding region
ENSG00000087884	Chromatin interaction
ENSG00000048649	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1045590	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11820337	0.80[ASW][hapmap];0.89[CHD][hapmap]
rs12225188	0.82[YRI][hapmap]
rs12788711	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2186562	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs28653530	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4145700	0.89[CHD][hapmap];0.89[YRI][hapmap]
rs516529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55190	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs567814	0.80[ASW][hapmap]
rs569072	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs572541	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs585513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs616354	0.80[ASW][hapmap];0.81[CHD][hapmap];0.82[YRI][hapmap]
rs618535	0.80[ASN][1000 genomes]
rs650636	0.80[ASW][hapmap];0.89[CHD][hapmap];0.83[JPT][hapmap];0.80[ASN][1000 genomes]
rs681411	0.82[JPT][hapmap]
rs7115444	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7117813	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7118800	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7119332	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7129325	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7931137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12417115	RSF1	cis	parietal	SCAN
rs12417115	DNAJB13	cis	parietal	SCAN
rs12417115	NEU3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77463800-77527000	Weak transcription	Aorta	Aorta
2	chr11:77475200-77527800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:77475400-77529000	Weak transcription	NHLF	lung
4	chr11:77475400-77530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr11:77495800-77528200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr11:77496000-77530200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr11:77501400-77526800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:77503600-77529600	Weak transcription	Right Ventricle	heart
9	chr11:77505000-77528400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr11:77506800-77528200	Weak transcription	Brain Hippocampus Middle	brain
11	chr11:77508000-77527800	Weak transcription	Colon Smooth Muscle	Colon
12	chr11:77509400-77528800	Weak transcription	Brain Germinal Matrix	brain
13	chr11:77509800-77530000	Weak transcription	NH-A	brain
14	chr11:77512000-77529600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr11:77512200-77529200	Weak transcription	Fetal Brain Female	brain
16	chr11:77512400-77530200	Weak transcription	Esophagus	oesophagus
17	chr11:77512400-77530600	Weak transcription	Lung	lung
18	chr11:77512600-77527000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:77512600-77530600	Weak transcription	Spleen	Spleen
20	chr11:77512800-77529800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:77512800-77530400	Weak transcription	Gastric	stomach
22	chr11:77513200-77529400	Weak transcription	Small Intestine	intestine
23	chr11:77515400-77530000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr11:77516600-77530200	Weak transcription	HSMM	muscle
25	chr11:77517200-77529200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:77518400-77527000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr11:77518400-77528400	Weak transcription	Osteobl	bone
28	chr11:77518400-77529200	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr11:77518600-77530000	Weak transcription	Brain Substantia Nigra	brain
30	chr11:77518800-77530000	Weak transcription	Colonic Mucosa	Colon
31	chr11:77519000-77527200	Weak transcription	HepG2	liver
32	chr11:77519000-77529400	Weak transcription	HUVEC	blood vessel
33	chr11:77519000-77530000	Weak transcription	Stomach Mucosa	stomach
34	chr11:77520000-77530000	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr11:77520200-77528800	Weak transcription	Fetal Brain Male	brain
36	chr11:77521200-77529800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr11:77521400-77528400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr11:77522200-77529400	Weak transcription	Left Ventricle	heart
39	chr11:77522400-77529800	Weak transcription	Fetal Kidney	kidney
40	chr11:77522600-77527000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:77522800-77527000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr11:77522800-77527000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr11:77522800-77528200	Weak transcription	Liver	Liver
44	chr11:77522800-77528400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:77522800-77529200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr11:77522800-77529400	Weak transcription	HSMMtube	muscle
47	chr11:77522800-77530000	Weak transcription	Adipose Nuclei	Adipose
48	chr11:77522800-77530200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr11:77523000-77528000	Weak transcription	Brain Anterior Caudate	brain
50	chr11:77523000-77529400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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