Variant report

Variant	rs6739840
Chromosome Location	chr2:183788369-183788370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183786363..183790600-chr2:183794242..183796759,3	K562	blood:
2	chr2:183787824..183790280-chr2:183794708..183796727,2	K562	blood:
3	chr2:183783194..183785818-chr2:183787179..183789437,2	MCF-7	breast:
4	chr2:183782658..183785008-chr2:183787087..183788615,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17265880	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2675089	0.85[EUR][1000 genomes]
rs35142583	0.91[AFR][1000 genomes]
rs66727515	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6711655	0.80[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6734848	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886535	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886536	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886547	0.91[AFR][1000 genomes]
rs72886597	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888442	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888444	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888445	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888452	0.84[AFR][1000 genomes]
rs72888453	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888459	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888467	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72888485	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72888487	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7575613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7595898	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7602601	0.82[AMR][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	nsv1009882	chr2:183213152-184171519	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2757842	chr2:183437700-183835084	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	esv2759104	chr2:183437700-183835084	Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv818096	chr2:183701588-183827018	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3693446	chr2:183785598-183833514	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6739840	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183757400-183797800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr2:183765200-183792800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:183765600-183805200	Weak transcription	Gastric	stomach
4	chr2:183768600-183811600	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:183769800-183811800	Weak transcription	Small Intestine	intestine
6	chr2:183772400-183791000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:183772400-183799200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:183772400-183811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
10	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
11	chr2:183773600-183793000	Weak transcription	Fetal Brain Male	brain
12	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
13	chr2:183779000-183792800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:183780000-183792800	Weak transcription	Psoas Muscle	Psoas
15	chr2:183780000-183807000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr2:183780400-183788400	Weak transcription	Brain Angular Gyrus	brain
17	chr2:183780400-183788600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr2:183780400-183790400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr2:183780400-183792400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:183780400-183800800	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
22	chr2:183780600-183791000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr2:183780600-183792800	Weak transcription	Ovary	ovary
24	chr2:183780800-183811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:183781000-183798200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:183781200-183788600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:183781200-183789800	Weak transcription	Brain Hippocampus Middle	brain
28	chr2:183781200-183791000	Weak transcription	NHLF	lung
29	chr2:183781200-183798200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr2:183781200-183805800	Weak transcription	Fetal Heart	heart
31	chr2:183781400-183790800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr2:183781400-183792200	Weak transcription	Hela-S3	cervix
33	chr2:183781400-183793000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:183781800-183790400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:183782200-183795400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr2:183782200-183814200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:183782400-183794600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:183783000-183799600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr2:183783200-183788800	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:183783800-183788400	Strong transcription	NHEK	skin
41	chr2:183784000-183788400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr2:183784200-183789800	Weak transcription	HMEC	breast
43	chr2:183784600-183788400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:183784600-183788400	Strong transcription	Fetal Stomach	stomach
45	chr2:183784600-183789200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:183784600-183804400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:183784800-183788400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:183784800-183788800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr2:183784800-183788800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:183784800-183811400	Strong transcription	Fetal Intestine Large	intestine

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