Variant report

Variant	rs7524967
Chromosome Location	chr1:227370823-227370824
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227365202..227367000-chr1:227368516..227370983,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADCK3-2	chr1:227370568-227371145	ENSG00000228625.1

Variant related genes	Relation type
ENSG00000228625	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs11799389	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800364	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800959	1.00[ASN][1000 genomes]
rs11801012	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801282	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802399	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11804181	0.81[AFR][1000 genomes]
rs11804807	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805012	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11805662	0.82[AMR][1000 genomes]
rs11806633	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11806721	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11807068	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11807375	1.00[ASN][1000 genomes]
rs11807425	1.00[ASN][1000 genomes]
rs11807957	1.00[ASN][1000 genomes]
rs11808210	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11808670	1.00[ASN][1000 genomes]
rs11808674	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11809113	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11809905	1.00[ASN][1000 genomes]
rs11810440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11811210	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11811620	1.00[ASN][1000 genomes]
rs11812048	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs12402400	1.00[ASN][1000 genomes]
rs12403978	1.00[ASN][1000 genomes]
rs12404219	1.00[ASN][1000 genomes]
rs12565212	0.82[YRI][hapmap]
rs17528049	1.00[ASN][1000 genomes]
rs17528077	1.00[ASN][1000 genomes]
rs1801783	1.00[ASN][1000 genomes]
rs2718199	0.82[YRI][hapmap]
rs34125608	1.00[ASN][1000 genomes]
rs35601687	1.00[ASN][1000 genomes]
rs36055753	0.81[AFR][1000 genomes]
rs3795452	0.82[YRI][hapmap]
rs41268741	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41268743	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270147	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45553032	1.00[ASN][1000 genomes]
rs55811522	1.00[ASN][1000 genomes]
rs56100227	1.00[ASN][1000 genomes]
rs61515455	1.00[ASN][1000 genomes]
rs61833999	1.00[ASN][1000 genomes]
rs61834000	1.00[ASN][1000 genomes]
rs61834003	1.00[ASN][1000 genomes]
rs61834008	1.00[ASN][1000 genomes]
rs61834038	1.00[ASN][1000 genomes]
rs66602251	1.00[ASN][1000 genomes]
rs6671926	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680937	1.00[ASN][1000 genomes]
rs73096355	1.00[ASN][1000 genomes]
rs73096357	1.00[ASN][1000 genomes]
rs7530155	1.00[ASN][1000 genomes]
rs7535648	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7547092	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9660532	1.00[CEU][hapmap];1.00[ASN][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	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7524967	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:227317000-227374200	Weak transcription	HepG2	liver
4	chr1:227329600-227380000	Weak transcription	Aorta	Aorta
5	chr1:227333400-227381000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr1:227333400-227405600	Weak transcription	Adipose Nuclei	Adipose
7	chr1:227334800-227371800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:227343200-227400400	Weak transcription	A549	lung
9	chr1:227346800-227379800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:227346800-227403800	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr1:227346800-227405800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:227346800-227406800	Weak transcription	Fetal Kidney	kidney
13	chr1:227347200-227378000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227347800-227385800	Weak transcription	Fetal Intestine Small	intestine
15	chr1:227347800-227390400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr1:227348200-227371400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:227348200-227376400	Weak transcription	Fetal Lung	lung
18	chr1:227348200-227377800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:227348200-227377800	Weak transcription	HUVEC	blood vessel
20	chr1:227348200-227379800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:227348200-227398000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:227348200-227398400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:227348200-227401600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:227348200-227408400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:227348200-227412200	Weak transcription	Fetal Muscle Leg	muscle
26	chr1:227348400-227378000	Weak transcription	Liver	Liver
27	chr1:227354800-227374400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:227355000-227374800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr1:227355400-227379800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr1:227355400-227386200	Weak transcription	Brain Anterior Caudate	brain
31	chr1:227357600-227374400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:227358600-227374000	Weak transcription	Left Ventricle	heart
33	chr1:227358800-227374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:227359200-227379600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:227359400-227374000	Weak transcription	Pancreas	Pancrea
36	chr1:227359400-227374400	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:227359400-227379800	Weak transcription	Brain Angular Gyrus	brain
38	chr1:227359400-227379800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr1:227359400-227379800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:227359400-227389000	Weak transcription	Right Ventricle	heart
41	chr1:227360800-227401200	Weak transcription	Hela-S3	cervix
42	chr1:227361200-227374200	Weak transcription	Psoas Muscle	Psoas
43	chr1:227362800-227377600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr1:227362800-227377800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr1:227362800-227379800	Weak transcription	NHLF	lung
46	chr1:227363000-227379600	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:227363800-227380600	Weak transcription	Esophagus	oesophagus
48	chr1:227364000-227379800	Weak transcription	HSMMtube	muscle
49	chr1:227364000-227385800	Weak transcription	Fetal Stomach	stomach
50	chr1:227364200-227381000	Weak transcription	Duodenum Mucosa	Duodenum

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