Variant report

Variant	rs17265866
Chromosome Location	chr2:183822374-183822375
allele	C/G
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	POLR2A	chr2:183821178-183822780	K562	blood:	n/a	n/a

Variant related genes	Relation type
NCKAP1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1561369	1.00[AFR][1000 genomes]
rs17265824	1.00[AFR][1000 genomes]
rs17265859	1.00[AFR][1000 genomes]
rs17265894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17703779	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2675073	0.87[CEU][hapmap]
rs41270217	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900703	1.00[AFR][1000 genomes]
rs7595898	0.87[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv1005281	chr2:183803173-184093877	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17265866	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183773400-183866000	Weak transcription	Colonic Mucosa	Colon
2	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
3	chr2:183775600-183833000	Weak transcription	Pancreas	Pancrea
4	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
5	chr2:183785800-183824200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:183786600-183826600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:183787000-183824000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:183788000-183830000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:183788200-183845600	Weak transcription	Lung	lung
10	chr2:183789200-183836400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr2:183790800-183824200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:183793400-183840800	Weak transcription	Fetal Brain Male	brain
13	chr2:183793600-183823800	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:183793600-183826600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:183795200-183824200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:183795400-183857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:183798600-183847000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:183803800-183826600	Weak transcription	Brain Germinal Matrix	brain
19	chr2:183803800-183826600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:183804800-183859600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr2:183805600-183874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr2:183807400-183824200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:183812000-183839000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:183812000-183857800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr2:183812200-183826200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:183812200-183826200	Weak transcription	Left Ventricle	heart
27	chr2:183812200-183826600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:183812200-183832800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:183812200-183833000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr2:183812200-183838200	Weak transcription	Small Intestine	intestine
31	chr2:183812200-183842000	Weak transcription	Right Ventricle	heart
32	chr2:183812200-183874800	Weak transcription	Gastric	stomach
33	chr2:183812400-183831200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr2:183812400-183856800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:183813400-183823200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:183813600-183823800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr2:183814400-183823600	Strong transcription	Adipose Nuclei	Adipose
38	chr2:183814600-183874800	Weak transcription	Aorta	Aorta
39	chr2:183814600-183893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:183814800-183824000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:183814800-183845600	Weak transcription	Ovary	ovary
42	chr2:183815000-183822600	Strong transcription	K562	blood
43	chr2:183815000-183824000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:183815000-183826600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr2:183815000-183833200	Weak transcription	Fetal Heart	heart
46	chr2:183815400-183826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr2:183815600-183822400	Strong transcription	A549	lung
48	chr2:183815800-183824200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:183815800-183832800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:183816000-183832800	Weak transcription	Psoas Muscle	Psoas

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