Variant report

Variant	rs2299628
Chromosome Location	chr11:17973607-17973608
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:17757400..17759383-chr11:17972395..17974521,2	K562	blood:

Variant related genes	Relation type
ENSG00000129159	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10741734	1.00[CEU][hapmap]
rs10766446	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11024435	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11024446	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11600873	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11603299	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11605018	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12292490	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12420936	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1401163	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1401164	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1401165	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1401166	1.00[CEU][hapmap]
rs1468291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1518521	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1607395	0.96[CEU][hapmap]
rs169806	0.96[CEU][hapmap]
rs17793542	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1800532	0.96[CEU][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap]
rs188397	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2041244	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2056246	0.92[CEU][hapmap];0.89[GIH][hapmap]
rs2097816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs211095	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211097	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211098	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211107	0.96[CEU][hapmap];0.82[GIH][hapmap];0.90[TSI][hapmap]
rs211128	1.00[YRI][hapmap]
rs211140	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211141	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs211144	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211146	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs211148	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211149	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211150	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211151	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2191091	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs2237909	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237911	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2237913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237914	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237915	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2237917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237920	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283233	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2283235	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283237	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299625	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2670764	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2670765	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs379388	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4141243	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4393297	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4757607	0.83[YRI][hapmap]
rs508924	0.96[CEU][hapmap]
rs511604	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs517005	0.92[CEU][hapmap];0.85[TSI][hapmap]
rs546383	0.96[CEU][hapmap];0.90[TSI][hapmap]
rs59573120	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs616099	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66813449	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs684302	0.92[CEU][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs685657	0.87[CEU][hapmap]
rs72862028	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs728639	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs739916	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7927135	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7933505	0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[TSI][hapmap]
rs887242	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs916975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9787863	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS 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	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2299628	SAAL1	cis	cerebellum	SCAN
rs2299628	HTATIP2	cis	parietal	SCAN
rs2299628	SERGEF	cis	normal skin	skin_eQTL
rs2299628	SERGEF	cis	Muscle Skeletal	GTEx
rs2299628	SAAL1	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17920600-17976000	Weak transcription	Esophagus	oesophagus
2	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
3	chr11:17937600-17977000	Weak transcription	Colon Smooth Muscle	Colon
4	chr11:17940000-17976400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:17943600-17975400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:17943800-17992800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr11:17944000-17975600	Weak transcription	HSMM	muscle
8	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:17945000-17974000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:17945200-17974800	Weak transcription	GM12878-XiMat	blood
11	chr11:17945400-17975400	Weak transcription	Pancreas	Pancrea
12	chr11:17945400-18010000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:17946200-17975400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr11:17948800-17981400	Weak transcription	Fetal Brain Male	brain
16	chr11:17949600-17974200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:17950200-17975600	Weak transcription	Fetal Stomach	stomach
18	chr11:17953400-17974800	Weak transcription	HSMMtube	muscle
19	chr11:17953400-17975400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr11:17954400-17975400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr11:17955400-17978200	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:17955600-17974000	Weak transcription	Stomach Mucosa	stomach
23	chr11:17956400-17975400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:17956800-17976800	Weak transcription	HMEC	breast
25	chr11:17957200-17994200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr11:17959200-18007600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr11:17961000-18016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:17962400-17975600	Weak transcription	Right Ventricle	heart
29	chr11:17962400-17976400	Weak transcription	Brain Angular Gyrus	brain
30	chr11:17963800-17976000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr11:17964200-17974800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr11:17965400-17994400	Weak transcription	NH-A	brain
33	chr11:17965800-17974000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr11:17965800-17974200	Weak transcription	Brain Anterior Caudate	brain
35	chr11:17965800-17974800	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr11:17966000-17976200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr11:17966000-17992600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr11:17966200-17975600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr11:17966200-17976000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:17966200-17976800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr11:17966400-17983400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:17966400-17984400	Strong transcription	Primary T cells from cord blood	blood
43	chr11:17966400-18014400	Weak transcription	Fetal Thymus	thymus
44	chr11:17966600-17994200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr11:17966800-17974000	Weak transcription	Dnd41	blood
46	chr11:17966800-17977600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:17966800-17984800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr11:17967400-17975000	Weak transcription	Hela-S3	cervix
49	chr11:17967400-17984400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr11:17967600-17974200	Weak transcription	Brain Germinal Matrix	brain

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