Variant report

Variant	rs959421
Chromosome Location	chr13:50062327-50062328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50060291..50062533-chr13:50067429..50069545,2	K562	blood:
2	chr13:50061212..50063170-chr13:50068743..50071652,2	MCF-7	breast:
3	chr13:50061049..50067624-chr13:50068104..50073631,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136147	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1409016	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1536194	0.81[EUR][1000 genomes]
rs1543514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1555530	0.86[EUR][1000 genomes]
rs1812	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs1853324	0.85[EUR][1000 genomes]
rs2031532	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs2057413	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2057415	0.86[EUR][1000 genomes]
rs2057417	0.86[EUR][1000 genomes]
rs2407692	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407693	0.94[ASN][1000 genomes]
rs3764090	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3764091	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4142285	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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4417458	0.90[ASN][1000 genomes]
rs4941642	0.80[EUR][1000 genomes]
rs4942835	0.87[ASN][1000 genomes]
rs6561525	0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6561527	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6561528	0.94[ASN][1000 genomes]
rs6561529	0.94[ASN][1000 genomes]
rs7139634	0.83[EUR][1000 genomes]
rs7321228	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7321670	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7324622	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7328782	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7330512	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7337488	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7982297	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7982598	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7987293	0.81[EUR][1000 genomes]
rs7992603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7994115	0.81[EUR][1000 genomes]
rs7996852	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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7998022	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7998427	0.81[EUR][1000 genomes]
rs7998660	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8000149	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9316453	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9526564	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535241	0.89[JPT][hapmap]
rs9535243	0.84[EUR][1000 genomes]
rs9535249	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9568219	0.86[EUR][1000 genomes]
rs967163	0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs967164	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv430562	chr13:49930643-50067246	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
rs959421	RNASEH2B	cis	parietal	SCAN
rs959421	EBPL	cis	parietal	SCAN
rs959421	SETDB2	cis	parietal	SCAN
rs959421	ARL11	cis	parietal	SCAN
rs959421	SETDB2	cis	cerebellum	SCAN
rs959421	RB1	cis	cerebellum	SCAN
rs959421	PHF11	Cis_1M	lymphoblastoid	RTeQTL
rs959421	CAB39L	cis	cerebellum	SCAN

Chromatin state (count:116 , 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	chr13:50023000-50068000	Weak transcription	Hela-S3	cervix
4	chr13:50031800-50068800	Weak transcription	Psoas Muscle	Psoas
5	chr13:50034400-50068800	Weak transcription	NH-A	brain
6	chr13:50036400-50068600	Weak transcription	Stomach Mucosa	stomach
7	chr13:50036600-50068000	Weak transcription	K562	blood
8	chr13:50037800-50064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:50037800-50068400	Weak transcription	HUVEC	blood vessel
10	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
11	chr13:50038000-50062800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr13:50038000-50063400	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr13:50038000-50063600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr13:50038000-50063800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr13:50038000-50068800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:50038200-50062400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:50038200-50063400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr13:50038400-50069000	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr13:50038400-50069400	Weak transcription	Small Intestine	intestine
22	chr13:50038600-50068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr13:50038800-50069000	Weak transcription	HSMM	muscle
24	chr13:50039000-50068200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:50039200-50068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:50039400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr13:50040600-50064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:50041000-50068800	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr13:50041400-50069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr13:50041600-50063800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr13:50042000-50063400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr13:50042200-50067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr13:50047400-50063400	Strong transcription	Liver	Liver
34	chr13:50047600-50063600	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr13:50048800-50063600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr13:50049400-50069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr13:50051200-50068400	Weak transcription	NHLF	lung
38	chr13:50051400-50069000	Weak transcription	Fetal Brain Female	brain
39	chr13:50051400-50069400	Weak transcription	Gastric	stomach
40	chr13:50051600-50068400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr13:50051800-50068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr13:50052000-50068800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr13:50052200-50069200	Weak transcription	Brain Germinal Matrix	brain
44	chr13:50052600-50069000	Weak transcription	Placenta	Placenta
45	chr13:50052600-50069200	Weak transcription	Brain Angular Gyrus	brain
46	chr13:50053000-50068600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr13:50053000-50069200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:50053000-50069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr13:50053000-50069400	Weak transcription	Esophagus	oesophagus
50	chr13:50053000-50069400	Weak transcription	Spleen	Spleen

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