Variant report

Variant	rs7338530
Chromosome Location	chr13:80051850-80051851
allele	C/T
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	CTCF	chr13:80051740-80051890	NHEK	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:80051040..80052592-chr13:80053663..80055858,2	K562	blood:
2	chr13:80051006..80052997-chr13:80053251..80055689,2	K562	blood:
3	chr13:80044193..80046856-chr13:80049312..80052188,3	K562	blood:

Variant related genes	Relation type
NDFIP2	TF binding region
ENSG00000102471	Chromatin interaction
ENSG00000232132	Chromatin interaction

Extended variants
information (count: 147 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs1208049	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1212082	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12865187	0.81[CHB][hapmap]
rs12871015	0.81[CHB][hapmap]
rs12877507	0.81[CHB][hapmap]
rs1324868	0.81[CHB][hapmap]
rs1335368	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1335370	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1408049	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1408658	0.81[CHB][hapmap]
rs1409018	0.81[CHB][hapmap]
rs1410336	0.81[CHB][hapmap]
rs1414155	0.87[ASN][1000 genomes]
rs1414156	0.87[ASN][1000 genomes]
rs1475797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1577416	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1577418	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17071512	1.00[YRI][hapmap]
rs17071545	1.00[YRI][hapmap]
rs1748761	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs1748768	0.81[CHB][hapmap]
rs1752648	0.81[CHB][hapmap]
rs1853830	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2025913	0.81[CHB][hapmap]
rs2057573	0.81[CHB][hapmap]
rs2065743	0.89[ASN][1000 genomes]
rs2182009	0.81[CHB][hapmap]
rs2182010	0.81[CHB][hapmap]
rs2182873	0.81[CHB][hapmap]
rs2265377	0.92[JPT][hapmap]
rs2265378	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2274555	0.81[CHB][hapmap]
rs2476173	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484343	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2484345	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2760101	0.88[ASN][1000 genomes]
rs2760102	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2760103	0.86[ASN][1000 genomes]
rs2760105	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760106	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2763809	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2763810	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2783119	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2783120	0.91[ASN][1000 genomes]
rs2783121	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2783122	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2783125	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2783126	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2876740	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs314687	0.85[ASN][1000 genomes]
rs314688	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3187338	0.81[CHB][hapmap]
rs3742117	0.87[CHB][hapmap]
rs3742118	0.80[CHB][hapmap]
rs3742119	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs3742122	0.81[CHB][hapmap]
rs3752994	0.81[CHB][hapmap]
rs3818563	0.81[CHB][hapmap]
rs386603	0.87[ASN][1000 genomes]
rs3903388	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs4145207	0.94[ASN][1000 genomes]
rs4146473	0.81[CHB][hapmap]
rs4476060	0.89[ASN][1000 genomes]
rs4885633	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4885634	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4885636	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs643778	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs6563098	0.81[CHB][hapmap]
rs6563100	0.81[CHB][hapmap]
rs6563104	0.81[CHB][hapmap]
rs6563110	0.82[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563113	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563115	0.91[ASN][1000 genomes]
rs6563116	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs700396	0.87[ASN][1000 genomes]
rs7317343	0.81[CHB][hapmap]
rs7317416	0.81[CHB][hapmap]
rs7319252	0.80[CHB][hapmap]
rs7319320	0.81[CHB][hapmap]
rs7321953	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7322167	0.81[CHB][hapmap]
rs7322673	0.81[CHB][hapmap]
rs73235963	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7325095	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7327386	0.80[CHB][hapmap]
rs7328494	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs7329331	0.81[CHB][hapmap]
rs7331872	0.81[CHB][hapmap]
rs7332367	0.81[CHB][hapmap]
rs7336581	0.81[CHB][hapmap]
rs7339303	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7981067	0.81[CHB][hapmap]
rs7982263	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7987193	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs7987769	0.81[CHB][hapmap]
rs7988601	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988784	0.81[CHB][hapmap]
rs7990344	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7996493	0.96[ASN][1000 genomes]
rs7996652	0.81[CHB][hapmap]
rs7998837	0.81[CHB][hapmap]
rs8001281	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs8002042	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs912639	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9318621	0.81[CHB][hapmap]
rs9318623	0.81[CHB][hapmap]
rs9318625	0.81[CHB][hapmap]
rs9318626	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs9318627	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs9318634	0.81[CHB][hapmap]
rs9318640	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9318641	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs9318644	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9530899	0.84[CHB][hapmap]
rs9530901	0.81[CHB][hapmap]
rs9530913	0.81[CHB][hapmap]
rs9530914	0.81[CHB][hapmap]
rs9530922	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9530925	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9545065	0.81[CHB][hapmap]
rs9545066	0.81[CHB][hapmap]
rs9545067	0.81[CHB][hapmap]
rs9545076	0.81[CHB][hapmap]
rs9545083	0.81[CHB][hapmap]
rs9545085	0.80[CHB][hapmap]
rs9545086	0.91[CEU][hapmap]
rs9545087	0.92[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap]
rs9545097	0.92[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs9545101	0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs9545142	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9565486	0.81[CHB][hapmap]
rs9565497	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs9565510	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9574409	0.81[CHB][hapmap]
rs9574413	1.00[YRI][hapmap]
rs9574416	0.81[CHB][hapmap]
rs9574418	0.82[AMR][1000 genomes]
rs9574422	0.92[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs9574429	0.89[ASN][1000 genomes]
rs9574434	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9593396	0.91[CEU][hapmap];0.81[CHB][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs9593399	0.89[ASN][1000 genomes]
rs9601240	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9601242	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs987284	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832657	chr13:79904978-80099108	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7338530	RP11-25J23.3	cis	Thyroid	GTEx
rs7338530	RBM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80048400-80053600	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr13:80050400-80054800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr13:80051600-80052000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr13:80051600-80052400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr13:80051600-80052600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:80051800-80052200	Flanking Active TSS	Fetal Heart	heart
7	chr13:80051800-80052400	Enhancers	HMEC	breast
8	chr13:80051800-80052600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr13:80051800-80052600	Enhancers	NHEK	skin
10	chr13:80051800-80052800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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