Variant report

Variant	rs10897488
Chromosome Location	chr11:64140806-64140807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64130858..64133466-chr11:64138873..64141793,3	K562	blood:
2	chr11:64140396..64140949-chr5:180454894..180455621,2	HCT-116	colon:
3	chr11:64122785..64130803-chr11:64136171..64143726,15	K562	blood:
4	chr11:64138832..64141064-chr11:64144568..64147426,2	K562	blood:
5	chr11:64129822..64132037-chr11:64139114..64141435,2	MCF-7	breast:
6	chr11:64140417..64141121-chr16:3073843..3074445,2	HCT-116	colon:
7	chr11:64140352..64141276-chr8:103667092..103668087,2	Hela-S3	cervix:
8	chr11:64140082..64140827-chr17:72634912..72635414,2	HCT-116	colon:
9	chr11:64121829..64128526-chr11:64138236..64143726,11	K562	blood:
10	chr11:64135284..64138280-chr11:64138462..64142226,6	K562	blood:
11	chr11:64139080..64141620-chr11:64144256..64148089,4	MCF-7	breast:
12	chr11:64140769..64142599-chr11:64166944..64169881,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000103145	Chromatin interaction
ENSG00000131652	Chromatin interaction
ENSG00000221273	Chromatin interaction
ENSG00000162302	Chromatin interaction
ENSG00000168071	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10792430	1.00[YRI][hapmap]
rs10897487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231771	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11542299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11601651	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601860	0.82[AMR][1000 genomes]
rs11606015	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1199045	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1199046	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1199047	0.85[EUR][1000 genomes]
rs1662188	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17857342	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2510066	0.87[ASW][hapmap];0.83[MEX][hapmap]
rs3132740	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474901	0.87[ASW][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs475032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479777	0.83[MEX][hapmap]
rs4930155	0.86[GIH][hapmap];0.83[MEX][hapmap]
rs499425	0.86[MEX][hapmap]
rs508168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510372	0.98[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs516124	1.00[ASW][hapmap];0.87[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs519763	0.87[ASW][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs521950	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs527465	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs538147	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs541207	0.89[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs542907	0.80[AMR][1000 genomes]
rs566128	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs574087	0.87[ASW][hapmap];0.87[MEX][hapmap]
rs574835	0.83[AMR][1000 genomes]
rs600377	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs612448	0.87[ASW][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.80[ASN][1000 genomes]
rs61886926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs645078	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647152	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs663743	0.86[ASW][hapmap]
rs694739	1.00[ASW][hapmap];0.83[MEX][hapmap]
rs72926005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72926006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs876064	0.88[YRI][hapmap]

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	esv1802079	chr11:63746066-64151373	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	247 gene(s)	inside rSNPs	diseases
2	nsv897646	chr11:63754986-64150370	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
3	nsv897662	chr11:63889749-64150370	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
4	nsv897664	chr11:63919742-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	237 gene(s)	inside rSNPs	diseases
5	nsv897671	chr11:63964657-64150370	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
6	nsv832186	chr11:63972260-64170059	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	180 gene(s)	inside rSNPs	diseases
7	esv1802320	chr11:63987425-64154633	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
8	nsv897679	chr11:63994692-64150370	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
9	nsv897682	chr11:63999529-64170500	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
10	nsv897685	chr11:64048912-64150370	Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
11	nsv897688	chr11:64107735-64150370	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv897689	chr11:64109118-64148420	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer 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 miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv832187	chr11:64121969-64312300	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10897488	CCS	cis	cerebellum	SCAN
rs10897488	CCDC88B	cis	lymphoblastoid	seeQTL
rs10897488	FKBP2	cis	parietal	SCAN
rs10897488	CCDC88B	cis	cerebellum	SCAN
rs10897488	CCDC88B	Cis_1M	lymphoblastoid	RTeQTL
rs10897488	FKBP2	cis	cerebellum	SCAN
rs10897488	SCGB2A2	cis	cerebellum	SCAN
rs10897488	C11orf68	cis	parietal	SCAN
rs10897488	C11orf68	cis	cerebellum	SCAN
rs10897488	CCDC88B	cis	parietal	SCAN
rs10897488	RPS6KA4	cis	cerebellar cortex	BrainEAC
rs10897488	PPP1CA	cis	parietal	SCAN
rs10897488	RPS6KA4	cis	thalamus	BrainEAC
rs10897488	RPS6KA4	cis	temporal cortex	BrainEAC
rs10897488	RPS6KA4	cis	brain	BrainEAC
rs10897488	TAF6L	cis	parietal	SCAN
rs10897488	CCDC88B	cis	multi-tissue	Pritchard
rs10897488	RPS6KA4	cis	frontal cortex	BrainEAC
rs10897488	AP003774.1	cis	Whole Blood	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64127400-64144400	Weak transcription	Psoas Muscle	Psoas
2	chr11:64127800-64146800	Weak transcription	Fetal Heart	heart
3	chr11:64130000-64142400	Weak transcription	Stomach Mucosa	stomach
4	chr11:64134400-64150200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr11:64134400-64158400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:64135600-64143000	Weak transcription	NH-A	brain
7	chr11:64135600-64145800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr11:64135600-64148800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr11:64136000-64145800	Weak transcription	HSMMtube	muscle
10	chr11:64138000-64141000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr11:64138000-64141200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr11:64138000-64142800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr11:64138000-64145800	Weak transcription	Osteobl	bone
14	chr11:64138000-64146000	Weak transcription	HMEC	breast
15	chr11:64138200-64141200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr11:64138200-64142600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:64138200-64146000	Weak transcription	Pancreas	Pancrea
18	chr11:64138200-64147200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr11:64138200-64151600	Weak transcription	Left Ventricle	heart
20	chr11:64138400-64142400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr11:64138400-64143800	Weak transcription	NHLF	lung
22	chr11:64138400-64144000	Weak transcription	Aorta	Aorta
23	chr11:64138600-64141200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:64138800-64146200	Weak transcription	Esophagus	oesophagus
25	chr11:64139000-64146000	Weak transcription	Right Ventricle	heart
26	chr11:64139200-64141000	Weak transcription	Fetal Muscle Leg	muscle
27	chr11:64139200-64141200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:64139200-64143000	Weak transcription	Small Intestine	intestine
29	chr11:64139400-64141200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr11:64139400-64141400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr11:64139400-64141400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr11:64139600-64142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:64139600-64145800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:64139600-64146200	Weak transcription	Gastric	stomach
35	chr11:64139600-64147400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr11:64139600-64148000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr11:64139800-64141200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:64139800-64145000	Weak transcription	Primary T cells from cord blood	blood
39	chr11:64139800-64145800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr11:64139800-64145800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:64139800-64147400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:64140000-64141200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr11:64140000-64141400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
44	chr11:64140000-64141400	Active TSS	Brain Angular Gyrus	brain
45	chr11:64140000-64141400	Active TSS	A549	lung
46	chr11:64140000-64141600	Weak transcription	Lung	lung
47	chr11:64140000-64142000	Weak transcription	Thymus	Thymus
48	chr11:64140000-64145400	Weak transcription	Fetal Brain Male	brain
49	chr11:64140000-64145800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:64140000-64145800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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