Variant report

Variant	rs9888511
Chromosome Location	chr13:39608900-39608901
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	WRNIP1	chr13:39608893-39609080	GM12878	blood:	n/a	n/a
2	CTCF	chr13:39608724-39609022	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:39599530..39604283-chr13:39604707..39609132,9	K562	blood:
2	chr13:39608105..39609639-chr13:40260400..40262356,2	K562	blood:

Variant related genes	Relation type
NHLRC3	TF binding region
PROSER1	TF binding region
ENSG00000133103	Chromatin interaction
ENSG00000120685	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11840611	0.95[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs12430086	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12857215	0.82[ASN][1000 genomes]
rs1326404	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1409442	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1536342	0.92[EUR][1000 genomes]
rs1853970	0.86[EUR][1000 genomes]
rs1887107	0.89[ASN][1000 genomes]
rs1887111	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1926474	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1926475	0.91[ASN][1000 genomes]
rs2094251	0.89[CEU][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs2148418	0.86[EUR][1000 genomes]
rs2324160	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751376	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3865000	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6563660	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs6563661	0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs6563662	0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs67948555	0.91[ASN][1000 genomes]
rs71439792	0.85[EUR][1000 genomes]
rs7320516	0.87[EUR][1000 genomes]
rs7324256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7324837	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7325996	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7337269	0.90[ASN][1000 genomes]
rs7489497	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7985641	0.89[ASW][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[YRI][hapmap];0.90[ASN][1000 genomes]
rs7995325	0.91[ASN][1000 genomes]
rs9315647	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs9315649	0.91[ASN][1000 genomes]
rs9315650	0.92[EUR][1000 genomes]
rs9566395	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576671	0.88[ASN][1000 genomes]
rs9576672	0.91[ASN][1000 genomes]
rs9576680	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9576687	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9576720	0.91[ASN][1000 genomes]
rs9576723	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9594319	0.91[ASN][1000 genomes]
rs9603500	0.91[ASN][1000 genomes]
rs9603503	0.92[EUR][1000 genomes]

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	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2753642	chr13:39522300-39649000	Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv2753553	chr13:39526600-39649000	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:39588600-39610400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:39589200-39609400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr13:39598000-39609600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:39598400-39609600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr13:39599800-39609000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:39599800-39609400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr13:39599800-39609400	Weak transcription	Fetal Stomach	stomach
8	chr13:39599800-39609400	Weak transcription	Gastric	stomach
9	chr13:39599800-39609400	Weak transcription	Right Ventricle	heart
10	chr13:39599800-39610400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:39599800-39610600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:39599800-39611200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr13:39600600-39610600	Weak transcription	Lung	lung
14	chr13:39602400-39609200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr13:39602400-39609200	Weak transcription	HSMMtube	muscle
16	chr13:39602400-39609400	Weak transcription	NH-A	brain
17	chr13:39603000-39609000	Weak transcription	Fetal Kidney	kidney
18	chr13:39603000-39609400	Weak transcription	Osteobl	bone
19	chr13:39603200-39609400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr13:39605400-39609400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr13:39605400-39609400	Weak transcription	Fetal Muscle Leg	muscle
22	chr13:39605600-39609400	Weak transcription	Placenta	Placenta
23	chr13:39606000-39609400	Weak transcription	Fetal Muscle Trunk	muscle
24	chr13:39606400-39609400	Weak transcription	HSMM	muscle
25	chr13:39606600-39609200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr13:39606600-39609400	Weak transcription	Psoas Muscle	Psoas
27	chr13:39607200-39610000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr13:39607400-39609400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr13:39607400-39609400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr13:39607600-39609600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr13:39607600-39609600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr13:39607800-39609400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:39608000-39609000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr13:39608000-39609200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr13:39608000-39609400	Enhancers	Brain Anterior Caudate	brain
36	chr13:39608200-39609200	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr13:39608200-39609200	Flanking Active TSS	GM12878-XiMat	blood
38	chr13:39608200-39609400	Enhancers	Primary T cells from cord blood	blood
39	chr13:39608200-39609400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr13:39608200-39609400	Enhancers	Brain Cingulate Gyrus	brain
41	chr13:39608200-39609400	Enhancers	Brain Hippocampus Middle	brain
42	chr13:39608200-39609400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr13:39608200-39609400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr13:39608200-39609600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr13:39608400-39609000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:39608400-39609000	Enhancers	NHEK	skin
47	chr13:39608400-39609200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr13:39608400-39609200	Enhancers	Small Intestine	intestine
49	chr13:39608400-39609200	Enhancers	NHLF	lung
50	chr13:39608400-39609400	Enhancers	H9 Cell Line	embryonic stem cell

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