Variant report

Variant	rs2450
Chromosome Location	chr2:153584421-153584422
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153581736..153584491-chr2:154342073..154344464,2	K562	blood:
2	chr2:153583102..153585171-chr2:153586170..153588194,2	MCF-7	breast:
3	chr2:153582588..153584915-chr2:153586087..153589184,3	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10169433	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10178613	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10193713	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13413144	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs13419134	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13427289	0.81[EUR][1000 genomes]
rs1437677	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4664120	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4664599	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4664608	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62179597	0.82[AFR][1000 genomes]
rs62179623	0.82[EUR][1000 genomes]
rs62179635	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62179636	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9989874	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1798142	chr2:153578113-153600123	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875293	chr2:153578900-153617420	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2450	NMI	cis	parietal	SCAN
rs2450	NCKAP5	trans	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153575800-153587200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:153575800-153611600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:153575800-153611600	Weak transcription	Esophagus	oesophagus
4	chr2:153575800-153621400	Weak transcription	Pancreas	Pancrea
5	chr2:153576000-153594400	Weak transcription	Left Ventricle	heart
6	chr2:153576000-153615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:153576200-153594800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:153576600-153587000	Weak transcription	Placenta	Placenta
9	chr2:153576800-153585200	Weak transcription	Fetal Stomach	stomach
10	chr2:153576800-153587200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr2:153576800-153591400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:153576800-153592600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:153576800-153592800	Weak transcription	NH-A	brain
14	chr2:153577000-153586400	Weak transcription	NHEK	skin
15	chr2:153577000-153587200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:153577000-153592600	Weak transcription	Fetal Intestine Large	intestine
17	chr2:153577000-153592800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:153577000-153593000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:153577000-153593000	Weak transcription	Osteobl	bone
20	chr2:153577000-153594400	Weak transcription	Aorta	Aorta
21	chr2:153577000-153594600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:153577000-153595000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr2:153577200-153584600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:153577200-153584800	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr2:153577200-153586200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr2:153577200-153586400	Weak transcription	Primary T cells from cord blood	blood
27	chr2:153577200-153587000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr2:153577200-153592800	Weak transcription	Brain Anterior Caudate	brain
29	chr2:153577200-153593000	Weak transcription	Fetal Kidney	kidney
30	chr2:153577200-153593000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:153577200-153593400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:153577200-153594200	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:153577200-153594600	Weak transcription	Spleen	Spleen
34	chr2:153577200-153617600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:153577400-153586200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr2:153577400-153586400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr2:153577400-153587200	Weak transcription	Thymus	Thymus
38	chr2:153577400-153593000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:153577400-153593400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:153577600-153585600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:153577600-153587000	Weak transcription	Fetal Thymus	thymus
42	chr2:153577600-153587200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr2:153577600-153594200	Weak transcription	Fetal Intestine Small	intestine
44	chr2:153577600-153617800	Weak transcription	NHLF	lung
45	chr2:153577800-153592800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr2:153577800-153593000	Weak transcription	Fetal Muscle Leg	muscle
47	chr2:153577800-153593000	Weak transcription	Ovary	ovary
48	chr2:153577800-153594800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr2:153578000-153585200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr2:153578200-153586400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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