Variant report

Variant	rs4941642
Chromosome Location	chr13:50039251-50039252
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50038863..50040866-chr13:50041548..50043299,2	K562	blood:
2	chr13:50027025..50029589-chr13:50038716..50040663,2	MCF-7	breast:
3	chr13:50038641..50040451-chr13:50143314..50145864,2	MCF-7	breast:
4	chr13:50017708..50019470-chr13:50036743..50039424,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12050042	0.94[ASN][1000 genomes]
rs1409016	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1536194	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1543514	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs1555530	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1980794	0.94[ASN][1000 genomes]
rs1980795	0.94[ASN][1000 genomes]
rs1998782	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2057413	0.80[EUR][1000 genomes]
rs2057415	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2057417	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2407689	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2407692	0.84[EUR][1000 genomes]
rs3764085	0.94[ASN][1000 genomes]
rs3764090	0.80[EUR][1000 genomes]
rs3794381	0.92[ASN][1000 genomes]
rs4142285	0.80[EUR][1000 genomes]
rs4468500	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4942831	0.96[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4942832	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6561525	0.84[EUR][1000 genomes]
rs71188363	0.88[ASN][1000 genomes]
rs7139634	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs721458	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7321228	0.80[EUR][1000 genomes]
rs7321670	0.82[EUR][1000 genomes]
rs7328782	0.83[EUR][1000 genomes]
rs7329078	0.88[ASN][1000 genomes]
rs7330512	0.80[EUR][1000 genomes]
rs7338755	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7982297	0.82[EUR][1000 genomes]
rs7982598	0.82[EUR][1000 genomes]
rs7987293	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7992603	0.81[EUR][1000 genomes]
rs7994115	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7994130	0.91[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7994566	0.91[CEU][hapmap]
rs7996852	0.81[EUR][1000 genomes]
rs7998427	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7998660	0.80[EUR][1000 genomes]
rs9316453	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs9526564	0.80[EUR][1000 genomes]
rs9535248	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535249	1.00[CEU][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9568219	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568223	0.94[ASN][1000 genomes]
rs959421	0.80[EUR][1000 genomes]
rs967163	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs967164	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	nsv430558	chr13:49914393-50059354	Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv430559	chr13:49930369-50059354	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv430560	chr13:49930643-50059354	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv430564	chr13:49945247-50059354	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	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
9	nsv430571	chr13:49961137-50059354	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4941642	PHF11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr13:50034400-50050800	Weak transcription	NHEK	skin
6	chr13:50034400-50052200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:50034400-50068800	Weak transcription	NH-A	brain
8	chr13:50034600-50039600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:50034800-50040400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr13:50035000-50040800	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr13:50035200-50039400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr13:50035200-50039400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr13:50035200-50042000	Strong transcription	Colon Smooth Muscle	Colon
14	chr13:50035200-50042200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr13:50035400-50040600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr13:50035600-50039400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:50035600-50039400	Strong transcription	Brain Hippocampus Middle	brain
18	chr13:50035600-50040400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr13:50035800-50040800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
20	chr13:50036400-50068600	Weak transcription	Stomach Mucosa	stomach
21	chr13:50036600-50068000	Weak transcription	K562	blood
22	chr13:50037000-50045600	Weak transcription	Fetal Heart	heart
23	chr13:50037600-50040800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr13:50037800-50040000	Strong transcription	Fetal Intestine Large	intestine
25	chr13:50037800-50041000	Strong transcription	Fetal Muscle Leg	muscle
26	chr13:50037800-50050200	Weak transcription	Osteobl	bone
27	chr13:50037800-50050600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr13:50037800-50050800	Weak transcription	Brain Angular Gyrus	brain
29	chr13:50037800-50051000	Weak transcription	Spleen	Spleen
30	chr13:50037800-50064000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr13:50037800-50068400	Weak transcription	HUVEC	blood vessel
32	chr13:50037800-50069000	Weak transcription	Colonic Mucosa	Colon
33	chr13:50038000-50039400	Strong transcription	Fetal Lung	lung
34	chr13:50038000-50039400	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr13:50038000-50040000	Weak transcription	Fetal Kidney	kidney
36	chr13:50038000-50040200	Weak transcription	Pancreas	Pancrea
37	chr13:50038000-50040400	Strong transcription	Ovary	ovary
38	chr13:50038000-50040400	Strong transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:50038000-50040600	Strong transcription	Thymus	Thymus
40	chr13:50038000-50041400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr13:50038000-50041600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr13:50038000-50041800	Strong transcription	Fetal Thymus	thymus
43	chr13:50038000-50043400	Weak transcription	Placenta	Placenta
44	chr13:50038000-50044600	Weak transcription	Fetal Stomach	stomach
45	chr13:50038000-50044600	Weak transcription	Lung	lung
46	chr13:50038000-50049000	Weak transcription	Gastric	stomach
47	chr13:50038000-50050200	Weak transcription	Esophagus	oesophagus
48	chr13:50038000-50050200	Weak transcription	HSMMtube	muscle
49	chr13:50038000-50050200	Weak transcription	NHLF	lung
50	chr13:50038000-50050800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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