Variant report

Variant	rs6734848
Chromosome Location	chr2:183866063-183866064
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183865248..183868928-chr2:183869372..183873704,5	K562	blood:
2	chr2:183865537..183868160-chr2:183888290..183890895,2	MCF-7	breast:
3	chr2:183865843..183868455-chr2:183901146..183903331,2	MCF-7	breast:
4	chr2:183865486..183867304-chr2:183885452..183887674,2	K562	blood:
5	chr2:183864377..183866340-chr2:183880546..183882680,2	K562	blood:
6	chr2:183843393..183845763-chr2:183864948..183867641,2	K562	blood:
7	chr2:183864297..183866939-chr2:183942510..183945015,2	K562	blood:

Variant related genes	Relation type
ENSG00000162999	Chromatin interaction
ENSG00000061676	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs17265880	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2675089	0.85[EUR][1000 genomes]
rs66727515	0.92[EUR][1000 genomes]
rs6711655	0.80[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6739840	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886535	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886536	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72886597	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888442	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888444	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888445	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888453	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888459	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72888467	0.95[EUR][1000 genomes]
rs72888485	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72888487	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7575613	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7595898	1.00[YRI][hapmap]

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	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
3	nsv875485	chr2:183827018-184195265	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1010799	chr2:183855680-184244721	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv536072	chr2:183855680-184244721	Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6734848	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:183773400-183877800	Weak transcription	Stomach Mucosa	stomach
2	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
3	chr2:183805600-183874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:183812200-183874800	Weak transcription	Gastric	stomach
5	chr2:183814600-183874800	Weak transcription	Aorta	Aorta
6	chr2:183814600-183893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:183827200-183874400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:183833600-183874800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:183833600-183874800	Weak transcription	Pancreas	Pancrea
10	chr2:183833600-183878400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:183833600-183879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr2:183836600-183867800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:183837000-183866600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:183837800-183866400	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr2:183838400-183867000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr2:183839800-183868400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:183841600-183868200	Strong transcription	HSMM	muscle
18	chr2:183842400-183874800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr2:183842600-183868800	Weak transcription	Right Ventricle	heart
20	chr2:183845200-183867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:183846000-183869800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:183846000-183902000	Weak transcription	Lung	lung
23	chr2:183847200-183867000	Strong transcription	HepG2	liver
24	chr2:183848000-183866600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:183852600-183874400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr2:183853000-183874800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:183853200-183874800	Weak transcription	Right Atrium	heart
28	chr2:183854000-183898800	Weak transcription	Fetal Brain Male	brain
29	chr2:183855400-183866600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:183855400-183866800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr2:183855400-183868200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:183855600-183874800	Weak transcription	Hela-S3	cervix
33	chr2:183856600-183867600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:183856800-183866200	Strong transcription	Fetal Intestine Large	intestine
35	chr2:183858400-183874800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:183858400-183874800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:183858600-183870400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:183859200-183866400	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:183859400-183872400	Weak transcription	Spleen	Spleen
40	chr2:183859600-183870600	Weak transcription	Brain Anterior Caudate	brain
41	chr2:183859600-183882000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:183859600-183899400	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr2:183861000-183874800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:183861600-183866600	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:183861800-183866800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:183862000-183869000	Strong transcription	K562	blood
47	chr2:183862400-183894400	Weak transcription	Placenta	Placenta
48	chr2:183863000-183874800	Weak transcription	Ovary	ovary
49	chr2:183864000-183866800	Strong transcription	Adipose Nuclei	Adipose
50	chr2:183864000-183867000	Strong transcription	Muscle Satellite Cultured Cells	--

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