Variant report

Variant	rs41270217
Chromosome Location	chr2:183850877-183850878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:183845824..183847389-chr2:183850200..183853171,2	K562	blood:
2	chr2:183849487..183851286-chr2:183867659..183869316,2	K562	blood:
3	chr2:183848253..183851068-chr2:183895481..183897989,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1561369	1.00[AFR][1000 genomes]
rs17265824	1.00[AFR][1000 genomes]
rs17265859	1.00[AFR][1000 genomes]
rs17265866	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17265894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17703779	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72900703	1.00[AFR][1000 genomes]
rs7595898	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41270217	NCKAP1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:99 , 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	chr2:183780400-183874800	Weak transcription	Esophagus	oesophagus
4	chr2:183795400-183857600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:183804800-183859600	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:183805600-183874400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:183812000-183857800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:183812200-183874800	Weak transcription	Gastric	stomach
9	chr2:183812400-183856800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:183814600-183874800	Weak transcription	Aorta	Aorta
11	chr2:183814600-183893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:183818600-183860400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:183827000-183859000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:183827200-183874400	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:183831400-183856000	Weak transcription	Fetal Stomach	stomach
16	chr2:183832000-183860000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr2:183833600-183864400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:183833600-183874800	Weak transcription	Brain Substantia Nigra	brain
19	chr2:183833600-183874800	Weak transcription	Pancreas	Pancrea
20	chr2:183833600-183878400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr2:183833600-183879600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr2:183836200-183851400	Strong transcription	HMEC	breast
23	chr2:183836200-183854000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:183836200-183854200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr2:183836200-183855200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:183836400-183854000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:183836400-183863400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:183836600-183851400	Strong transcription	NH-A	brain
29	chr2:183836600-183867800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:183836800-183851200	Strong transcription	Osteobl	bone
31	chr2:183836800-183858000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:183837000-183863400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:183837000-183866600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:183837200-183860800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr2:183837800-183851200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:183837800-183866400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:183838000-183854200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:183838400-183867000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:183838600-183865600	Weak transcription	Small Intestine	intestine
40	chr2:183839000-183851400	Strong transcription	HUVEC	blood vessel
41	chr2:183839000-183852600	Weak transcription	Brain Germinal Matrix	brain
42	chr2:183839400-183855200	Strong transcription	Fetal Intestine Large	intestine
43	chr2:183839400-183858000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:183839600-183864400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:183839800-183868400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr2:183840600-183851400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr2:183840800-183855600	Strong transcription	NHDF-Ad	bronchial
48	chr2:183840800-183864200	Weak transcription	Fetal Brain Female	brain
49	chr2:183841200-183861000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr2:183841600-183868200	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links