Variant report

Variant	rs1144840
Chromosome Location	chr1:226819833-226819834
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10495246	1.00[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1144838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144839	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]
rs1151804	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1288936	0.85[JPT][hapmap]
rs17522524	1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17588687	0.90[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3768376	0.90[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs3820635	0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3820637	0.90[CHB][hapmap];0.83[JPT][hapmap];0.90[EUR][1000 genomes]
rs697843	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7533764	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470779	chr1:226778432-226833304	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv873234	chr1:226779449-226859676	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv522446	chr1:226785530-226923938	Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv873235	chr1:226819073-226851963	Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1144840	CABC1	cis	cerebellum	SCAN
rs1144840	PARP1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226806200-226825800	Weak transcription	Right Atrium	heart
2	chr1:226810600-226822600	Weak transcription	Gastric	stomach
3	chr1:226814200-226820600	Weak transcription	Right Ventricle	heart
4	chr1:226814200-226821400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:226814200-226823600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:226814200-226837600	Weak transcription	HUVEC	blood vessel
7	chr1:226814400-226820200	Weak transcription	Primary hematopoietic stem cells	blood
8	chr1:226814400-226821600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr1:226814600-226820000	Weak transcription	Dnd41	blood
10	chr1:226814600-226824200	Weak transcription	Brain Angular Gyrus	brain
11	chr1:226814600-226824800	Weak transcription	Liver	Liver
12	chr1:226814800-226820400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:226814800-226820600	Weak transcription	Brain Anterior Caudate	brain
14	chr1:226814800-226821200	Weak transcription	Adipose Nuclei	Adipose
15	chr1:226814800-226821600	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:226814800-226830400	Strong transcription	Thymus	Thymus
17	chr1:226814800-226834800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:226814800-226840600	Weak transcription	Small Intestine	intestine
19	chr1:226815000-226820000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:226815000-226820000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:226815000-226820000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:226815000-226820400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr1:226815000-226821600	Weak transcription	Esophagus	oesophagus
24	chr1:226815000-226823800	Weak transcription	Ovary	ovary
25	chr1:226815200-226821400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:226816000-226820000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr1:226816000-226820400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:226816400-226820200	Strong transcription	Primary T cells from cord blood	blood
29	chr1:226816400-226820600	Strong transcription	Fetal Thymus	thymus
30	chr1:226816800-226820800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:226816800-226837000	Weak transcription	Fetal Brain Male	brain
32	chr1:226817000-226820200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:226817000-226837000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr1:226817200-226820000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr1:226817200-226825400	Strong transcription	Lung	lung
36	chr1:226817200-226828000	Weak transcription	Fetal Brain Female	brain
37	chr1:226817200-226830600	Strong transcription	Fetal Intestine Small	intestine
38	chr1:226817600-226820400	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr1:226817600-226820600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:226817600-226820600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:226817600-226821400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr1:226817800-226821200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:226817800-226821400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr1:226817800-226822800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr1:226817800-226828000	Weak transcription	Aorta	Aorta
46	chr1:226818000-226820000	Weak transcription	Brain Substantia Nigra	brain
47	chr1:226818000-226820400	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:226818000-226820400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:226818000-226821200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr1:226818000-226824400	Weak transcription	Fetal Lung	lung

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