Variant report

Variant	rs4941643
Chromosome Location	chr13:50068387-50068388
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50019424..50021164-chr13:50065782..50068488,2	MCF-7	breast:
2	chr13:49993633..49996417-chr13:50068251..50070383,2	K562	blood:
3	chr13:50068064..50069672-chr13:50174689..50176260,2	MCF-7	breast:
4	chr13:50061049..50067624-chr13:50068104..50073631,8	MCF-7	breast:
5	chr13:50060291..50062533-chr13:50067429..50069545,2	K562	blood:
6	chr13:50020071..50022197-chr13:50067941..50070115,2	K562	blood:
7	chr13:50064832..50068654-chr13:50068754..50072882,4	K562	blood:

Variant related genes	Relation type
ENSG00000236577	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136147	Chromatin interaction
ENSG00000215462	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11619265	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12429813	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs1409017	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1543513	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17073051	0.88[CEU][hapmap]
rs2038638	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2057414	0.88[CEU][hapmap];0.82[CHB][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2057416	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2077848	0.94[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2407691	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2981	0.81[CEU][hapmap]
rs35980977	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764084	0.84[EUR][1000 genomes]
rs3764089	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4340215	0.85[CEU][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes]
rs4430650	0.85[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4942830	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4942833	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]
rs61959992	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561526	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561533	0.89[CEU][hapmap]
rs7139494	0.88[CEU][hapmap]
rs721457	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7317772	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7326345	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7990988	0.81[CEU][hapmap]
rs7991031	0.81[CEU][hapmap]
rs7991226	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7995283	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7997737	0.88[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9316454	0.88[CEU][hapmap];0.81[CHB][hapmap];0.86[EUR][1000 genomes]
rs9526563	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535247	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9535251	0.90[ASN][1000 genomes]
rs9805560	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4941643	CAB39L	cis	cerebellum	SCAN
rs4941643	RCBTB1	cis	multi-tissue	Pritchard
rs4941643	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs4941643	PHF11	cis	multi-tissue	Pritchard
rs4941643	CAB39L	Cis_1M	lymphoblastoid	RTeQTL
rs4941643	SETDB2	cis	cerebellum	SCAN
rs4941643	SETDB2	cis	multi-tissue	Pritchard
rs4941643	RB1	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50020200-50068400	Weak transcription	HMEC	breast
2	chr13:50022000-50069000	Weak transcription	Fetal Brain Male	brain
3	chr13:50031800-50068800	Weak transcription	Psoas Muscle	Psoas
4	chr13:50034400-50068800	Weak transcription	NH-A	brain
5	chr13:50036400-50068600	Weak transcription	Stomach Mucosa	stomach
6	chr13:50037800-50068400	Weak transcription	HUVEC	blood vessel
7	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
8	chr13:50038000-50068800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:50038400-50069000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:50038400-50069400	Weak transcription	Small Intestine	intestine
11	chr13:50038600-50068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:50038800-50069000	Weak transcription	HSMM	muscle
13	chr13:50039200-50068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr13:50039400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr13:50041000-50068800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr13:50041400-50069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:50049400-50069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr13:50051200-50068400	Weak transcription	NHLF	lung
19	chr13:50051400-50069000	Weak transcription	Fetal Brain Female	brain
20	chr13:50051400-50069400	Weak transcription	Gastric	stomach
21	chr13:50051600-50068400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:50051800-50068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr13:50052000-50068800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr13:50052200-50069200	Weak transcription	Brain Germinal Matrix	brain
25	chr13:50052600-50069000	Weak transcription	Placenta	Placenta
26	chr13:50052600-50069200	Weak transcription	Brain Angular Gyrus	brain
27	chr13:50053000-50068600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr13:50053000-50069200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr13:50053000-50069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:50053000-50069400	Weak transcription	Esophagus	oesophagus
31	chr13:50053000-50069400	Weak transcription	Spleen	Spleen
32	chr13:50053400-50069200	Weak transcription	Brain Substantia Nigra	brain
33	chr13:50055400-50068600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr13:50055400-50069000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr13:50056000-50068400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr13:50056400-50068400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr13:50057200-50069200	Weak transcription	Colon Smooth Muscle	Colon
38	chr13:50059000-50069000	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:50059200-50068600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr13:50059400-50068800	Weak transcription	Brain Anterior Caudate	brain
41	chr13:50060000-50068400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr13:50060000-50069200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr13:50060800-50068400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr13:50060800-50069000	Weak transcription	Right Ventricle	heart
45	chr13:50061000-50068600	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr13:50061000-50068600	Weak transcription	Thymus	Thymus
47	chr13:50061000-50069000	Weak transcription	Aorta	Aorta
48	chr13:50061000-50069200	Weak transcription	Pancreas	Pancrea
49	chr13:50061000-50069400	Weak transcription	HSMMtube	muscle
50	chr13:50061200-50068600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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