Variant report

Variant	rs1357468
Chromosome Location	chr2:152683731-152683732
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152682999..152684816-chr2:152835840..152837979,2	K562	blood:
2	chr2:152623919..152627757-chr2:152680404..152683778,4	K562	blood:
3	chr2:152615779..152617906-chr2:152682702..152684733,2	K562	blood:
4	chr2:152655109..152656955-chr2:152681729..152684723,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10167462	0.94[ASW][hapmap];0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10170273	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs10178880	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs10193188	0.87[CEU][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap]
rs1054883	0.93[CEU][hapmap];0.95[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11683122	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11683683	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11695661	0.87[CEU][hapmap];0.90[GIH][hapmap]
rs12052828	0.87[CEU][hapmap]
rs12464543	0.87[CEU][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap]
rs12616767	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs12620077	0.80[CEU][hapmap];0.83[GIH][hapmap]
rs13015219	0.82[ASN][1000 genomes]
rs13032138	0.80[CEU][hapmap]
rs13404704	0.80[CEU][hapmap]
rs1523180	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1799	0.93[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2344733	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2345154	0.85[ASN][1000 genomes]
rs4077121	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs4077122	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs4267505	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4273217	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4349344	0.81[ASN][1000 genomes]
rs4355107	0.81[ASN][1000 genomes]
rs4374369	0.87[CEU][hapmap]
rs4381781	0.87[CEU][hapmap]
rs4413159	0.87[CEU][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap]
rs4425075	0.87[CEU][hapmap]
rs4465763	0.87[CEU][hapmap];0.81[JPT][hapmap]
rs4508593	0.81[ASN][1000 genomes]
rs4508594	0.81[ASN][1000 genomes]
rs4536649	0.80[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap]
rs4564766	0.87[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap]
rs4611637	0.87[CEU][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap]
rs4614931	0.83[ASW][hapmap];0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];0.80[YRI][hapmap];0.81[ASN][1000 genomes]
rs4625904	0.87[CEU][hapmap]
rs4664494	0.83[GIH][hapmap]
rs4664497	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs4664501	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs56229257	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6433569	0.88[GIH][hapmap];0.81[MEX][hapmap]
rs6433575	0.87[CEU][hapmap]
rs6433603	0.80[ASN][1000 genomes]
rs6433606	0.81[ASN][1000 genomes]
rs6433610	0.81[ASN][1000 genomes]
rs6713162	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs6716286	0.87[CEU][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap]
rs6729101	0.89[ASW][hapmap];0.93[CEU][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap]
rs6730589	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs6733909	0.87[CEU][hapmap];0.88[GIH][hapmap]
rs6734148	0.87[CEU][hapmap];0.90[GIH][hapmap];0.87[MEX][hapmap]
rs6735208	0.87[CEU][hapmap]
rs6760384	0.87[CEU][hapmap];0.90[JPT][hapmap]
rs7426114	0.80[CEU][hapmap]
rs7563441	0.87[CEU][hapmap];0.85[JPT][hapmap]
rs7564024	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs7567785	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7596744	0.93[CEU][hapmap];0.95[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9287990	0.80[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap]
rs9789671	0.89[AMR][1000 genomes];0.93[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	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	esv3693431	chr2:152683731-152981827	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1357468	NEB	cis	parietal	SCAN
rs1357468	STAM2	cis	cerebellar cortex	BrainEAC

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152675200-152684000	Weak transcription	Esophagus	oesophagus
2	chr2:152675200-152684000	Weak transcription	Lung	lung
3	chr2:152680600-152684000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:152680600-152684000	Weak transcription	Pancreas	Pancrea
5	chr2:152680600-152684000	Weak transcription	Spleen	Spleen
6	chr2:152681400-152684000	Weak transcription	Gastric	stomach
7	chr2:152682200-152683800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:152682200-152684000	Flanking Active TSS	HUVEC	blood vessel
9	chr2:152682600-152683800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr2:152682800-152683800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr2:152682800-152683800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr2:152682800-152683800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:152682800-152683800	Flanking Active TSS	NH-A	brain
14	chr2:152682800-152684000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:152682800-152684000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr2:152682800-152684000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:152682800-152684000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
18	chr2:152682800-152684200	Flanking Active TSS	Dnd41	blood
19	chr2:152682800-152685200	Active TSS	Fetal Intestine Large	intestine
20	chr2:152682800-152685200	Active TSS	GM12878-XiMat	blood
21	chr2:152682800-152685200	Active TSS	HMEC	breast
22	chr2:152682800-152685400	Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr2:152682800-152685400	Active TSS	Aorta	Aorta
24	chr2:152682800-152685600	Active TSS	Right Atrium	heart
25	chr2:152683000-152683800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:152683000-152683800	Flanking Active TSS	Fetal Heart	heart
27	chr2:152683000-152683800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr2:152683000-152684000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr2:152683000-152684000	Flanking Active TSS	Brain Anterior Caudate	brain
30	chr2:152683000-152684000	Flanking Active TSS	Brain Hippocampus Middle	brain
31	chr2:152683000-152684000	Flanking Active TSS	Fetal Lung	lung
32	chr2:152683000-152684000	Flanking Active TSS	Osteobl	bone
33	chr2:152683000-152684200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr2:152683000-152684400	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr2:152683000-152684400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:152683000-152684400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:152683000-152684600	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr2:152683000-152684600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr2:152683000-152685200	Active TSS	Fetal Intestine Small	intestine
40	chr2:152683000-152685600	Active TSS	NHLF	lung
41	chr2:152683000-152685800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:152683200-152683800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
43	chr2:152683200-152683800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:152683200-152683800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:152683200-152683800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
46	chr2:152683200-152683800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:152683200-152683800	Flanking Active TSS	Brain Angular Gyrus	brain
48	chr2:152683200-152683800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr2:152683200-152683800	Flanking Active TSS	Fetal Kidney	kidney
50	chr2:152683200-152683800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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