Variant report

Variant	rs4942833
Chromosome Location	chr13:50081358-50081359
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50068457..50070652-chr13:50081260..50083175,3	MCF-7	breast:
2	chr13:50072641..50077099-chr13:50079863..50082927,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1046027	0.89[GIH][hapmap]
rs1046028	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs1046295	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs11619265	0.83[CHB][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs12429813	0.84[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes]
rs12429883	0.90[JPT][hapmap]
rs1409017	0.94[EUR][1000 genomes]
rs1543513	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs17073051	0.96[CEU][hapmap]
rs2038638	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs2057414	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2057416	0.93[EUR][1000 genomes]
rs2077848	0.81[CEU][hapmap];0.87[MEX][hapmap];0.81[EUR][1000 genomes]
rs2247119	0.80[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2274277	0.80[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs2407691	0.83[EUR][1000 genomes]
rs2980	0.88[CEU][hapmap];0.86[GIH][hapmap]
rs2981	0.92[CEU][hapmap];0.87[GIH][hapmap]
rs3186012	0.84[CEU][hapmap]
rs3186013	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs3186024	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs35980977	0.87[EUR][1000 genomes]
rs3764084	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3764089	0.88[EUR][1000 genomes]
rs3765526	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3829366	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs4340215	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4430650	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4941643	0.89[CEU][hapmap];0.83[CHB][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4942830	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs6561526	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6561533	0.92[CEU][hapmap];0.83[YRI][hapmap]
rs6561534	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7139494	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs721457	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs7317772	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7317982	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7322077	0.81[CEU][hapmap]
rs7323493	0.80[EUR][1000 genomes]
rs7323716	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7326345	0.81[EUR][1000 genomes]
rs7337718	0.80[EUR][1000 genomes]
rs7339167	0.80[EUR][1000 genomes]
rs7990988	0.92[CEU][hapmap]
rs7991031	0.92[CEU][hapmap];0.90[GIH][hapmap]
rs7991226	0.81[EUR][1000 genomes]
rs7995283	0.81[CEU][hapmap];0.91[MEX][hapmap];0.83[EUR][1000 genomes]
rs7995684	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7997737	0.84[CEU][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes]
rs9316454	0.84[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs942870	0.80[EUR][1000 genomes]
rs9526563	0.83[EUR][1000 genomes]
rs9526565	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9526567	0.92[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9526568	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9535247	0.83[CEU][hapmap]
rs9535254	0.81[CEU][hapmap]
rs9535255	0.81[CEU][hapmap]
rs9805560	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv430561	chr13:49930643-50089844	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430566	chr13:49945247-50089844	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430570	chr13:49961137-50089844	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv523648	chr13:50005444-50086266	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv561613	chr13:50013622-50086266	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv900070	chr13:50013622-50087142	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv561614	chr13:50042983-50086253	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv561615	chr13:50042983-50086266	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers 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	9 gene(s)	inside rSNPs	diseases
12	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4942833	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs4942833	SETDB2	cis	cerebellum	SCAN
rs4942833	KCNRG	cis	cerebellum	SCAN
rs4942833	CCDC70	cis	cerebellum	SCAN
rs4942833	RB1	cis	cerebellum	SCAN
rs4942833	CAB39L	cis	cerebellum	SCAN
rs4942833	RCBTB1	cis	multi-tissue	Pritchard
rs4942833	CAB39L	Cis_1M	lymphoblastoid	RTeQTL
rs4942833	PHF11	cis	multi-tissue	Pritchard

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50070200-50089200	Weak transcription	Fetal Brain Male	brain
2	chr13:50070800-50086600	Weak transcription	Psoas Muscle	Psoas
3	chr13:50070800-50086800	Weak transcription	Ovary	ovary
4	chr13:50070800-50087400	Weak transcription	Placenta	Placenta
5	chr13:50070800-50087600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr13:50070800-50087800	Weak transcription	Aorta	Aorta
7	chr13:50070800-50087800	Weak transcription	NHEK	skin
8	chr13:50070800-50088000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr13:50070800-50088000	Weak transcription	Brain Anterior Caudate	brain
10	chr13:50070800-50088000	Weak transcription	Esophagus	oesophagus
11	chr13:50070800-50088000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr13:50070800-50088200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr13:50070800-50088200	Weak transcription	Brain Substantia Nigra	brain
14	chr13:50070800-50095600	Weak transcription	Fetal Kidney	kidney
15	chr13:50071000-50087800	Weak transcription	Colonic Mucosa	Colon
16	chr13:50071000-50087800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr13:50071000-50087800	Weak transcription	Right Ventricle	heart
18	chr13:50071000-50088000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:50071000-50093400	Weak transcription	HepG2	liver
20	chr13:50071200-50081600	Weak transcription	Thymus	Thymus
21	chr13:50071400-50081600	Weak transcription	Fetal Muscle Leg	muscle
22	chr13:50071400-50087000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr13:50071400-50087200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr13:50071800-50087200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr13:50071800-50088000	Weak transcription	Pancreas	Pancrea
26	chr13:50073800-50081600	Weak transcription	Liver	Liver
27	chr13:50074000-50093000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr13:50074600-50081400	Weak transcription	Dnd41	blood
29	chr13:50074800-50086400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr13:50075000-50086800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr13:50075000-50087000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr13:50075000-50087800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr13:50075000-50087800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr13:50075000-50088200	Weak transcription	HMEC	breast
35	chr13:50075000-50102400	Weak transcription	NH-A	brain
36	chr13:50075000-50143800	Weak transcription	Small Intestine	intestine
37	chr13:50075200-50081400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr13:50075200-50087800	Weak transcription	Osteobl	bone
39	chr13:50075400-50088000	Weak transcription	Colon Smooth Muscle	Colon
40	chr13:50077400-50083600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:50077400-50087800	Weak transcription	Left Ventricle	heart
42	chr13:50077600-50081600	Weak transcription	HUVEC	blood vessel
43	chr13:50077600-50086600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr13:50077600-50086800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr13:50077600-50088000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:50077600-50088000	Weak transcription	Gastric	stomach
47	chr13:50077600-50088000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:50077600-50088000	Weak transcription	Spleen	Spleen
49	chr13:50077600-50114000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr13:50077800-50081400	Weak transcription	GM12878-XiMat	blood

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