Variant report

Variant	rs13213544
Chromosome Location	chr6:167321657-167321658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BHLHE40	chr6:167321522-167321804	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:167321487-167322013	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:167316933..167319053-chr6:167320800..167322909,2	K562	blood:
2	chr6:167320098..167322424-chr6:167348297..167350309,2	K562	blood:

Variant related genes	Relation type
RPS6KA2	TF binding region
ENSG00000231654	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11159	0.82[EUR][1000 genomes]
rs13201493	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201941	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202098	0.84[EUR][1000 genomes]
rs13216122	0.92[TSI][hapmap]
rs13220568	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34101156	0.87[EUR][1000 genomes]
rs34116393	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34159386	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34431091	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35147976	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35206089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35614625	0.87[EUR][1000 genomes]
rs35615089	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35731380	0.85[EUR][1000 genomes]
rs36032379	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58251236	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59988493	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60908348	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6916542	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71571463	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71571464	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71571465	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs71571466	0.95[EUR][1000 genomes]
rs7740833	0.85[EUR][1000 genomes]
rs7755545	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9295378	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9295379	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9295380	0.81[EUR][1000 genomes]
rs9295382	0.87[EUR][1000 genomes]
rs9457239	0.87[EUR][1000 genomes]
rs9457243	0.98[EUR][1000 genomes]
rs9457244	0.85[EUR][1000 genomes]
rs9457245	0.84[EUR][1000 genomes]
rs9459799	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9459800	0.85[EUR][1000 genomes]
rs9459802	0.85[EUR][1000 genomes]
rs9459803	0.85[EUR][1000 genomes]
rs9459804	0.87[EUR][1000 genomes]
rs9459806	0.85[EUR][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	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1022866	chr6:167108740-167345629	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv482525	chr6:167151805-167324406	Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv605327	chr6:167185674-167360389	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1027314	chr6:167194653-167355961	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv538542	chr6:167194653-167355961	Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv605332	chr6:167198027-167353701	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
11	nsv605333	chr6:167201033-167321693	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13213544	C11orf21	trans	lymphoblastoid	seeQTL
rs13213544	RPS6KA2	cis	multi-tissue	Pritchard

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167315800-167341600	Weak transcription	Pancreas	Pancrea
2	chr6:167318400-167343800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:167318600-167323400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr6:167318600-167342400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr6:167318800-167324400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:167318800-167326800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:167319000-167321800	Weak transcription	Brain Germinal Matrix	brain
8	chr6:167319200-167327600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:167320200-167322000	Enhancers	Primary T cells fromperipheralblood	blood
10	chr6:167320200-167322200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:167320200-167322200	Enhancers	Fetal Thymus	thymus
12	chr6:167320200-167322400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:167320200-167322600	Enhancers	Brain Anterior Caudate	brain
14	chr6:167320200-167323000	Enhancers	Primary B cells from peripheral blood	blood
15	chr6:167320400-167321800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:167320400-167322000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:167320400-167322000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:167320400-167322200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr6:167320400-167322200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr6:167320400-167322600	Enhancers	Spleen	Spleen
21	chr6:167320400-167322800	Enhancers	Primary B cells from cord blood	blood
22	chr6:167320400-167326000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:167320400-167327400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr6:167320600-167321800	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr6:167320600-167321800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr6:167320600-167321800	Enhancers	K562	blood
27	chr6:167320600-167322400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:167320600-167323000	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr6:167320800-167321800	Enhancers	Brain Angular Gyrus	brain
30	chr6:167320800-167322400	Enhancers	Primary hematopoietic stem cells	blood
31	chr6:167320800-167322600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr6:167320800-167322600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:167320800-167322600	Enhancers	Placenta	Placenta
34	chr6:167321200-167321800	Enhancers	Brain Cingulate Gyrus	brain
35	chr6:167321200-167322000	Enhancers	Gastric	stomach
36	chr6:167321200-167322600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr6:167321200-167322600	Enhancers	Brain Hippocampus Middle	brain
38	chr6:167321200-167323000	Enhancers	Ovary	ovary
39	chr6:167321200-167326000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:167321200-167327800	Weak transcription	Brain Substantia Nigra	brain
41	chr6:167321200-167340000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:167321400-167322000	Enhancers	Primary T cells from cord blood	blood
43	chr6:167321400-167322000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr6:167321400-167322200	Enhancers	Adipose Nuclei	Adipose
45	chr6:167321400-167322400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr6:167321400-167322600	Enhancers	GM12878-XiMat	blood
47	chr6:167321400-167326000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr6:167321600-167321800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:167321600-167321800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr6:167321600-167322000	Enhancers	Brain Inferior Temporal Lobe	brain

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