Variant report

Variant	rs967164
Chromosome Location	chr13:50062110-50062111
allele	A/T
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: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12050042	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1409016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536194	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1543514	0.81[CEU][hapmap]
rs1555530	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980794	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1980795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1998782	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057413	0.86[EUR][1000 genomes]
rs2057415	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2407689	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407692	0.81[EUR][1000 genomes]
rs3764085	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794381	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4142285	0.86[EUR][1000 genomes]
rs4468500	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4941642	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4942831	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4942832	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6561525	0.81[EUR][1000 genomes]
rs71188363	0.92[ASN][1000 genomes]
rs7139634	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721458	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7318481	0.88[YRI][hapmap]
rs7321228	0.86[EUR][1000 genomes]
rs7329078	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7338755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7987293	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7994115	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7994130	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7994566	0.91[CEU][hapmap]
rs7996852	0.86[EUR][1000 genomes]
rs7998427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9316453	0.81[CEU][hapmap]
rs9526564	0.86[EUR][1000 genomes]
rs9526569	0.90[JPT][hapmap]
rs9535248	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568219	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568223	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959421	0.86[EUR][1000 genomes]
rs967163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs967164	PHF11	Cis_1M	lymphoblastoid	RTeQTL

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	chr13:50038400-50062200	Strong transcription	Primary T cells from cord blood	blood
19	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr13:50038400-50066800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:50038400-50069000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:50038400-50069400	Weak transcription	Small Intestine	intestine
23	chr13:50038600-50068800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:50038800-50069000	Weak transcription	HSMM	muscle
25	chr13:50039000-50068200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr13:50039200-50068800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr13:50039400-50069200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:50040600-50064800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:50041000-50068800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr13:50041400-50069400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:50041600-50063800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr13:50042000-50063400	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr13:50042200-50067000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr13:50047400-50063400	Strong transcription	Liver	Liver
35	chr13:50047600-50063600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr13:50048800-50063600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr13:50049400-50069000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr13:50051200-50068400	Weak transcription	NHLF	lung
39	chr13:50051400-50069000	Weak transcription	Fetal Brain Female	brain
40	chr13:50051400-50069400	Weak transcription	Gastric	stomach
41	chr13:50051600-50068400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr13:50051800-50068800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr13:50052000-50068800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr13:50052200-50069200	Weak transcription	Brain Germinal Matrix	brain
45	chr13:50052600-50069000	Weak transcription	Placenta	Placenta
46	chr13:50052600-50069200	Weak transcription	Brain Angular Gyrus	brain
47	chr13:50053000-50068600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr13:50053000-50069200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:50053000-50069400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr13:50053000-50069400	Weak transcription	Esophagus	oesophagus

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