Variant report

Variant	rs663649
Chromosome Location	chr1:70897183-70897184
allele	G/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	FOXA1	chr1:70896988-70897332	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:70891788..70893936-chr1:70895573..70898086,2	K562	blood:

Variant related genes	Relation type
CTH	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10458561	0.81[EUR][1000 genomes]
rs10889869	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10889871	0.82[EUR][1000 genomes]
rs1145919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590089	0.88[EUR][1000 genomes]
rs12029858	0.82[EUR][1000 genomes]
rs1967189	0.81[EUR][1000 genomes]
rs4650049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4650051	0.82[EUR][1000 genomes]
rs473334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs515064	0.91[CEU][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs525919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs583316	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9633291	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv461828	chr1:70880717-70922360	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv546456	chr1:70880717-70922360	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs663649	LRRC40	cis	cerebellum	SCAN
rs663649	CTH	Cis_1M	lymphoblastoid	RTeQTL
rs663649	LRRIQ3	cis	parietal	SCAN
rs663649	SRSF11	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70877400-70898600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:70877400-70900600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:70877400-70900600	Weak transcription	Lung	lung
4	chr1:70877400-70901800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:70877400-70903400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:70877400-70906400	Weak transcription	Small Intestine	intestine
7	chr1:70877400-70906600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:70877800-70907800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:70878000-70899000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:70878000-70903400	Weak transcription	Primary hematopoietic stem cells	blood
11	chr1:70878000-70908200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:70878200-70899200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:70878200-70907000	Weak transcription	Psoas Muscle	Psoas
14	chr1:70878200-70909600	Weak transcription	Gastric	stomach
15	chr1:70878400-70897600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr1:70878400-70897600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:70878400-70897800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr1:70878400-70899200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:70878400-70901800	Weak transcription	Colonic Mucosa	Colon
20	chr1:70878400-70907000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:70878600-70902600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:70878600-70903800	Weak transcription	HSMMtube	muscle
23	chr1:70878600-70906000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:70878800-70897200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:70878800-70897200	Weak transcription	Dnd41	blood
26	chr1:70878800-70897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:70878800-70897800	Weak transcription	Brain Substantia Nigra	brain
28	chr1:70878800-70897800	Weak transcription	Right Ventricle	heart
29	chr1:70878800-70899000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:70878800-70901000	Weak transcription	Fetal Kidney	kidney
31	chr1:70878800-70902200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:70880000-70897600	Weak transcription	Brain Germinal Matrix	brain
33	chr1:70881800-70897200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr1:70884400-70909000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr1:70884600-70898800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:70884600-70899000	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr1:70884600-70899400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr1:70884600-70902800	Weak transcription	Osteobl	bone
39	chr1:70886400-70906600	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:70886400-70906800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr1:70888000-70906000	Weak transcription	Fetal Brain Male	brain
42	chr1:70890600-70898800	Weak transcription	NH-A	brain
43	chr1:70891400-70907400	Weak transcription	Fetal Stomach	stomach
44	chr1:70892200-70897800	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:70892200-70907400	Weak transcription	Fetal Brain Female	brain
46	chr1:70892400-70897600	Weak transcription	Brain Anterior Caudate	brain
47	chr1:70892400-70906400	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr1:70892600-70897600	Weak transcription	Left Ventricle	heart
49	chr1:70892600-70897800	Weak transcription	Fetal Muscle Leg	muscle
50	chr1:70892600-70897800	Weak transcription	HepG2	liver

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