Variant report

Variant	rs41268743
Chromosome Location	chr1:227327527-227327528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:227321877..227323599-chr1:227327325..227328877,2	K562	blood:
2	chr1:227316215..227319084-chr1:227324943..227327660,2	K562	blood:
3	chr1:227327253..227330264-chr1:227332146..227336856,4	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11549708	1.00[ASN][1000 genomes]
rs11799389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800169	0.82[EUR][1000 genomes]
rs11800364	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11800959	1.00[ASN][1000 genomes]
rs11801012	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11801282	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11802399	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11803919	0.85[EUR][1000 genomes]
rs11804181	0.82[EUR][1000 genomes]
rs11804807	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805012	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11805662	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11806633	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11807375	1.00[ASN][1000 genomes]
rs11807425	1.00[ASN][1000 genomes]
rs11807957	1.00[ASN][1000 genomes]
rs11809113	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11810440	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11811210	1.00[ASN][1000 genomes]
rs11811620	1.00[ASN][1000 genomes]
rs11812048	1.00[ASN][1000 genomes]
rs12402400	1.00[ASN][1000 genomes]
rs12403978	1.00[ASN][1000 genomes]
rs12404219	1.00[ASN][1000 genomes]
rs1317490	1.00[ASN][1000 genomes]
rs17528049	1.00[ASN][1000 genomes]
rs17528077	1.00[ASN][1000 genomes]
rs1801783	1.00[ASN][1000 genomes]
rs34125608	1.00[ASN][1000 genomes]
rs35601687	1.00[ASN][1000 genomes]
rs41268741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41270147	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41303131	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]
rs61833991	1.00[ASN][1000 genomes]
rs61833993	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];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680937	1.00[ASN][1000 genomes]
rs6704087	1.00[ASN][1000 genomes]
rs73096355	1.00[ASN][1000 genomes]
rs73096357	1.00[ASN][1000 genomes]
rs7524967	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530155	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535648	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547092	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv832792	chr1:227211378-227364992	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv873239	chr1:227222125-227361072	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv468227	chr1:227223736-227340790	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv549269	chr1:227223736-227340790	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv873240	chr1:227228946-227361072	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873241	chr1:227242247-227361072	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv549270	chr1:227290139-227361072	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	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
11	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
rs41268743	CDC42BPA	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
2	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
3	chr1:227272800-227331000	Weak transcription	Lung	lung
4	chr1:227286400-227328200	Weak transcription	Brain Germinal Matrix	brain
5	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
6	chr1:227288200-227332400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:227288400-227343000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:227288400-227398000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr1:227288600-227328200	Weak transcription	Fetal Stomach	stomach
10	chr1:227288600-227332400	Weak transcription	NHLF	lung
11	chr1:227288600-227333600	Weak transcription	Esophagus	oesophagus
12	chr1:227288800-227330000	Weak transcription	NHDF-Ad	bronchial
13	chr1:227295200-227346400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr1:227298600-227351800	Weak transcription	Hela-S3	cervix
15	chr1:227299800-227332600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr1:227300000-227328600	Weak transcription	Fetal Brain Female	brain
17	chr1:227300000-227329200	Weak transcription	Aorta	Aorta
18	chr1:227300000-227333800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:227300000-227379800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:227300200-227334400	Weak transcription	Stomach Mucosa	stomach
21	chr1:227311000-227329200	Weak transcription	Pancreas	Pancrea
22	chr1:227311000-227329400	Weak transcription	Fetal Intestine Small	intestine
23	chr1:227314000-227327800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:227314200-227327800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr1:227314200-227327800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:227314200-227329400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr1:227316600-227352200	Weak transcription	Gastric	stomach
28	chr1:227316800-227328200	Weak transcription	Left Ventricle	heart
29	chr1:227316800-227328400	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:227316800-227329000	Weak transcription	Placenta	Placenta
31	chr1:227316800-227329200	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:227316800-227331000	Weak transcription	HSMMtube	muscle
33	chr1:227317000-227374200	Weak transcription	HepG2	liver
34	chr1:227317200-227328200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr1:227317200-227331000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr1:227317600-227331000	Weak transcription	NHEK	skin
37	chr1:227318200-227329000	Weak transcription	Fetal Kidney	kidney
38	chr1:227319600-227332400	Weak transcription	Brain Angular Gyrus	brain
39	chr1:227319800-227330600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:227320400-227327600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr1:227323200-227342600	Weak transcription	Colon Smooth Muscle	Colon
42	chr1:227323200-227346400	Weak transcription	Brain Substantia Nigra	brain
43	chr1:227323400-227328600	Weak transcription	Ovary	ovary
44	chr1:227323400-227330600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:227324200-227348400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr1:227325200-227333800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:227325400-227333400	Strong transcription	Adipose Nuclei	Adipose
48	chr1:227325400-227334400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:227325400-227334800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:227325400-227335200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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