Variant report

Variant	rs6561552
Chromosome Location	chr13:50260905-50260906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50254223..50257561-chr13:50258855..50261948,4	K562	blood:
2	chr13:50260531..50263061-chr13:50365546..50368292,2	K562	blood:
3	chr13:50252667..50256255-chr13:50260389..50264756,4	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11148164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11148167	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1127021	0.93[CEU][hapmap];0.90[YRI][hapmap]
rs1211304	0.87[GIH][hapmap]
rs12428108	1.00[JPT][hapmap]
rs12584401	0.91[JPT][hapmap]
rs12864534	0.91[ASN][1000 genomes]
rs12866447	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs12877931	0.91[ASN][1000 genomes]
rs1407440	0.81[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs1407441	0.81[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs1581745	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs1923730	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs2146143	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2181185	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs2236354	0.91[JPT][hapmap]
rs35331571	0.88[ASN][1000 genomes]
rs4643206	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4941657	0.91[JPT][hapmap]
rs4942863	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs4942864	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs6561550	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561553	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6561560	0.85[CEU][hapmap];0.87[GIH][hapmap]
rs73192666	1.00[ASN][1000 genomes]
rs7446	0.82[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs7983303	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs7984061	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs7987502	0.83[JPT][hapmap]
rs7997798	0.82[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs9316474	0.81[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs942032	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526592	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9526593	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs9535287	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535301	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9535305	0.93[CEU][hapmap];0.85[YRI][hapmap]
rs9535307	0.93[CEU][hapmap];0.84[YRI][hapmap]
rs9535310	0.81[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];0.86[YRI][hapmap]
rs9535315	0.91[ASN][1000 genomes]
rs9535326	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9535332	0.83[JPT][hapmap]
rs9535333	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs9535341	0.87[GIH][hapmap];0.81[YRI][hapmap]
rs9535347	0.91[JPT][hapmap]
rs9562927	0.87[GIH][hapmap];0.81[YRI][hapmap]
rs9568309	0.92[ASN][1000 genomes]
rs9646001	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv541772	chr13:50218255-50264414	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6561552	STK32C	trans	cerebellum	SCAN
rs6561552	TRIM13	Cis_1M	lymphoblastoid	RTeQTL
rs6561552	HTR2A	cis	parietal	SCAN
rs6561552	KCNRG	cis	cerebellum	SCAN
rs6561552	EBPL	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50241000-50264800	Weak transcription	Aorta	Aorta
2	chr13:50242200-50261000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr13:50242200-50261400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr13:50242200-50264200	Weak transcription	K562	blood
5	chr13:50242200-50264400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr13:50242200-50264400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr13:50242400-50261400	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr13:50242400-50261400	Weak transcription	Gastric	stomach
9	chr13:50242400-50262200	Weak transcription	Spleen	Spleen
10	chr13:50242400-50263200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:50242400-50263800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr13:50242400-50264000	Weak transcription	Thymus	Thymus
13	chr13:50242400-50264400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr13:50242400-50264400	Weak transcription	Adipose Nuclei	Adipose
15	chr13:50242400-50264400	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr13:50244400-50264400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr13:50245800-50261400	Weak transcription	HUVEC	blood vessel
18	chr13:50246000-50264600	Weak transcription	Left Ventricle	heart
19	chr13:50246200-50261400	Weak transcription	Hela-S3	cervix
20	chr13:50247000-50264400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr13:50248400-50263600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr13:50249400-50263600	Weak transcription	Primary B cells from cord blood	blood
23	chr13:50250400-50264400	Weak transcription	Primary T cells from cord blood	blood
24	chr13:50251400-50264400	Weak transcription	Primary B cells from peripheral blood	blood
25	chr13:50251600-50264400	Weak transcription	HSMMtube	muscle
26	chr13:50251800-50262200	Weak transcription	Pancreas	Pancrea
27	chr13:50251800-50263600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:50253600-50264800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:50253800-50261400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr13:50253800-50264000	Weak transcription	Ovary	ovary
31	chr13:50253800-50264400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:50253800-50264400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr13:50254000-50264400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:50254400-50261200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:50254400-50264400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr13:50254400-50264400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr13:50254400-50264400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr13:50254400-50264600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr13:50254400-50264600	Weak transcription	Esophagus	oesophagus
40	chr13:50254600-50261200	Weak transcription	A549	lung
41	chr13:50254600-50261400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:50254600-50264200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr13:50255200-50264400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr13:50255400-50261400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:50256000-50262000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr13:50256200-50264600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr13:50256400-50261200	Weak transcription	HSMM	muscle
48	chr13:50256400-50261200	Weak transcription	Osteobl	bone
49	chr13:50256400-50263800	Weak transcription	NH-A	brain
50	chr13:50256400-50263800	Weak transcription	NHLF	lung

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