Variant report

Variant	rs660442
Chromosome Location	chr11:64042997-64042998
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	POLR2A	chr11:64042569-64043500	Hela-S3	cervix:	n/a	n/a
2	TFAP2C	chr11:64042883-64043608	Hela-S3	cervix:	n/a	chr11:64043003-64043018
3	POLR2A	chr11:64042467-64043719	SK-N-MC	brain:	n/a	n/a
4	CTCF	chr11:64042920-64043070	WERI-Rb-1	eye:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:64041009..64043331-chr11:64125161..64128159,2	MCF-7	breast:
2	chr11:64032072..64048684-chr11:64048768..64055711,68	MCF-7	breast:
3	chr11:64040946..64043668-chr11:64061691..64063928,2	MCF-7	breast:
4	chr11:64033188..64045448-chr11:64059274..64075790,38	MCF-7	breast:
5	chr11:64042595..64046939-chr11:64049156..64053929,8	MCF-7	breast:
6	chr11:63951667..63955297-chr11:64041322..64044678,4	MCF-7	breast:

Variant related genes	Relation type
GPR137	TF binding region
BAD	TF binding region
ENSG00000173264	Chromatin interaction
ENSG00000207024	Chromatin interaction
ENSG00000219435	Chromatin interaction
ENSG00000182450	Chromatin interaction
ENSG00000168439	Chromatin interaction
ENSG00000162302	Chromatin interaction
ENSG00000002330	Chromatin interaction
ENSG00000173153	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs2286613	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3759057	1.00[AFR][1000 genomes]
rs61886887	1.00[AFR][1000 genomes]
rs61886930	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897631	chr11:63664882-64129722	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer 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	254 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1035875	chr11:63800238-64132030	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS 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	234 gene(s)	inside rSNPs	diseases
5	nsv469961	chr11:63822940-64085967	Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
6	nsv897660	chr11:63860826-64125142	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	231 gene(s)	inside rSNPs	diseases
7	nsv897661	chr11:63863405-64129722	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
8	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
9	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
10	nsv468592	chr11:63924446-64042997	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
11	nsv555184	chr11:63924446-64042997	Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	166 gene(s)	inside rSNPs	diseases
12	nsv869944	chr11:63932152-64123062	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
13	nsv468593	chr11:63941734-64089874	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
14	nsv555185	chr11:63941734-64089874	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription 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 target site	212 gene(s)	inside rSNPs	diseases
15	nsv555186	chr11:63949095-64097233	Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	212 gene(s)	inside rSNPs	diseases
16	nsv897667	chr11:63964657-64078380	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
17	nsv897668	chr11:63964657-64085298	Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	163 gene(s)	inside rSNPs	diseases
18	nsv897669	chr11:63964657-64089874	Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
19	nsv897670	chr11:63964657-64097233	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
20	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
21	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
22	nsv897672	chr11:63979643-64082807	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS 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 target site	140 gene(s)	inside rSNPs	diseases
23	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
24	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
25	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
26	nsv1043277	chr11:64002997-64132030	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs660442	CCDC88B	cis	lymphoblastoid	seeQTL
rs660442	FKBP2	cis	parietal	SCAN
rs660442	FKBP2	cis	cerebellum	SCAN
rs660442	CYBASC3	cis	cerebellum	SCAN
rs660442	CTSW	cis	cerebellum	SCAN
rs660442	ZFPL1	cis	cerebellum	SCAN
rs660442	TAF6L	cis	parietal	SCAN
rs660442	AP003774.1	cis	Whole Blood	GTEx
rs660442	CCDC88B	cis	cerebellum	SCAN
rs660442	PPP1CA	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64039400-64043200	Weak transcription	Aorta	Aorta
2	chr11:64039400-64044200	Weak transcription	Small Intestine	intestine
3	chr11:64039400-64044400	Enhancers	Stomach Mucosa	stomach
4	chr11:64039600-64043000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:64039600-64043000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:64039600-64043000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:64039600-64043000	Weak transcription	Esophagus	oesophagus
8	chr11:64039600-64043000	Weak transcription	Left Ventricle	heart
9	chr11:64039600-64043000	Weak transcription	NHDF-Ad	bronchial
10	chr11:64039600-64043000	Weak transcription	NHEK	skin
11	chr11:64039600-64044000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:64039600-64044200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr11:64039600-64044200	Weak transcription	Right Atrium	heart
14	chr11:64039600-64046200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr11:64039600-64049000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr11:64039600-64050400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr11:64039600-64050800	Weak transcription	Psoas Muscle	Psoas
18	chr11:64039600-64051000	Weak transcription	Fetal Kidney	kidney
19	chr11:64039600-64051000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:64039600-64051400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr11:64039600-64051400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr11:64039600-64051600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:64039800-64043000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr11:64039800-64043000	Weak transcription	HMEC	breast
25	chr11:64039800-64043400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr11:64039800-64043400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr11:64039800-64044000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:64039800-64044200	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr11:64039800-64044400	Weak transcription	Primary T cells from cord blood	blood
30	chr11:64039800-64044400	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr11:64039800-64044400	Weak transcription	HSMMtube	muscle
32	chr11:64039800-64044400	Weak transcription	NH-A	brain
33	chr11:64039800-64044600	Weak transcription	Brain Angular Gyrus	brain
34	chr11:64039800-64049000	Weak transcription	Colon Smooth Muscle	Colon
35	chr11:64039800-64050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr11:64039800-64050800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr11:64039800-64051000	Weak transcription	Primary B cells from cord blood	blood
38	chr11:64039800-64051000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:64039800-64051000	Weak transcription	HSMM	muscle
40	chr11:64039800-64051000	Weak transcription	HUVEC	blood vessel
41	chr11:64039800-64051400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr11:64040000-64043000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr11:64040000-64043000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr11:64040000-64049000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:64040000-64050600	Strong transcription	Fetal Stomach	stomach
46	chr11:64040000-64050800	Weak transcription	Fetal Brain Male	brain
47	chr11:64040000-64051200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr11:64040200-64043000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr11:64040200-64043000	Weak transcription	Spleen	Spleen
50	chr11:64040200-64043000	Weak transcription	Osteobl	bone

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