Variant report

Variant	rs660070
Chromosome Location	chr11:63863405-63863406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63854748..63858551-chr11:63863184..63865147,4	K562	blood:
2	chr11:63862447..63864017-chr11:63864274..63865912,2	K562	blood:
3	chr11:63861818..63863709-chr11:63865717..63867837,2	MCF-7	breast:
4	chr11:63861047..63863678-chr11:63899191..63900819,2	MCF-7	breast:
5	chr11:63862716..63865369-chr11:63868424..63871611,3	K562	blood:
6	chr11:63862168..63865369-chr11:63868424..63871008,4	K562	blood:

Variant related genes	Relation type
ENSG00000126500	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10897465	1.00[YRI][hapmap]
rs11231662	1.00[YRI][hapmap]
rs11231664	1.00[YRI][hapmap]
rs11231670	1.00[YRI][hapmap]
rs11231713	1.00[ASW][hapmap]
rs11605797	1.00[YRI][hapmap]
rs12786124	1.00[YRI][hapmap]
rs12800703	1.00[YRI][hapmap]
rs1807304	0.89[CEU][hapmap]
rs2005261	0.81[CEU][hapmap]
rs2096706	1.00[ASW][hapmap]
rs2186572	1.00[YRI][hapmap]
rs2701542	0.84[CEU][hapmap]
rs2845889	0.81[CEU][hapmap]
rs492357	1.00[YRI][hapmap]
rs4980499	1.00[YRI][hapmap]
rs4980500	1.00[YRI][hapmap]
rs504060	1.00[YRI][hapmap]
rs509701	1.00[YRI][hapmap]
rs582692	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617856	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs646384	1.00[ASW][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs683996	0.81[CHD][hapmap]
rs876064	1.00[ASW][hapmap]
rs915987	1.00[ASW][hapmap]
rs947939	1.00[ASW][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897629	chr11:63664882-63866959	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv897630	chr11:63664882-63924446	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	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
4	esv1849906	chr11:63719273-63880383	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv29993	chr11:63738642-63864211	Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv897642	chr11:63744152-63866959	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv897651	chr11:63761169-63863405	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
10	nsv897652	chr11:63761169-63866959	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv897653	chr11:63761169-63875456	Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
12	nsv897654	chr11:63772000-63875456	Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv832184	chr11:63787702-63925084	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	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
15	nsv897657	chr11:63810944-63866959	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv897658	chr11:63810944-63897759	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	nsv897659	chr11:63813470-63907079	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv832185	chr11:63819946-63963532	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	89 gene(s)	inside rSNPs	diseases
19	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
20	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
21	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs660070	KCNK4	cis	parietal	SCAN
rs660070	ANKRD13D	cis	cerebellum	SCAN
rs660070	FKBP2	cis	parietal	SCAN
rs660070	FKBP2	cis	cerebellum	SCAN
rs660070	TMEM216	cis	parietal	SCAN
rs660070	ESRRA	cis	cerebellum	SCAN
rs660070	CCDC88B	cis	cerebellum	SCAN
rs660070	RAB1B	cis	cerebellum	SCAN
rs660070	RCE1	cis	cerebellum	SCAN
rs660070	RBM14	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63848200-63865600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr11:63851800-63868400	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr11:63853000-63869000	Enhancers	Brain Hippocampus Middle	brain
4	chr11:63853000-63871200	Enhancers	Brain Cingulate Gyrus	brain
5	chr11:63853000-63871600	Enhancers	Brain Substantia Nigra	brain
6	chr11:63853400-63871200	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr11:63853600-63864400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:63853600-63870800	Enhancers	Brain Angular Gyrus	brain
9	chr11:63854600-63864400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr11:63854600-63868400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr11:63855400-63864800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:63856400-63871400	Enhancers	Brain Anterior Caudate	brain
13	chr11:63856800-63864000	Enhancers	Adipose Nuclei	Adipose
14	chr11:63857400-63864000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:63857400-63864800	Enhancers	Fetal Muscle Leg	muscle
16	chr11:63857400-63866800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:63858000-63864000	Enhancers	Placenta	Placenta
18	chr11:63859200-63866200	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr11:63859400-63864600	Enhancers	Brain Germinal Matrix	brain
20	chr11:63860200-63867000	Enhancers	Colon Smooth Muscle	Colon
21	chr11:63860800-63863800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:63861200-63866400	Enhancers	Rectal Smooth Muscle	rectum
23	chr11:63861400-63864000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr11:63861400-63864000	Enhancers	Fetal Lung	lung
25	chr11:63861800-63866600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr11:63862000-63863600	Enhancers	Fetal Thymus	thymus
27	chr11:63862000-63863800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr11:63862000-63863800	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr11:63862000-63866000	Enhancers	Fetal Brain Male	brain
30	chr11:63862000-63866600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr11:63862200-63863800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr11:63862200-63863800	Enhancers	Primary hematopoietic stem cells	blood
33	chr11:63862200-63864000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr11:63862200-63864800	Enhancers	Lung	lung
35	chr11:63862200-63865000	Weak transcription	HepG2	liver
36	chr11:63862200-63865200	Enhancers	Psoas Muscle	Psoas
37	chr11:63862400-63863800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr11:63862400-63864400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr11:63862400-63865400	Weak transcription	Esophagus	oesophagus
40	chr11:63862400-63866000	Enhancers	Fetal Brain Female	brain
41	chr11:63862600-63863600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr11:63862800-63863600	Enhancers	Colonic Mucosa	Colon
43	chr11:63863000-63863600	Enhancers	Fetal Intestine Large	intestine
44	chr11:63863000-63863800	Enhancers	Fetal Heart	heart
45	chr11:63863000-63863800	Enhancers	Fetal Intestine Small	intestine
46	chr11:63863000-63863800	Enhancers	Spleen	Spleen
47	chr11:63863000-63864400	Enhancers	Pancreas	Pancrea
48	chr11:63863000-63864600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
49	chr11:63863000-63865600	Enhancers	Right Ventricle	heart
50	chr11:63863200-63866800	Bivalent Enhancer	Fetal Stomach	stomach

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