Variant report

Variant	rs11097408
Chromosome Location	chr4:95165662-95165663
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	chr4:95157684..95160378-chr4:95163793..95166793,3	K562	blood:
2	chr4:95149538..95151966-chr4:95163560..95166301,2	K562	blood:

Extended variants
information (count: 169 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:167)

rs_ID	r²[population]
rs10000247	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10008044	0.91[ASN][1000 genomes]
rs10016806	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10018905	0.84[AFR][1000 genomes]
rs10023115	0.91[ASN][1000 genomes]
rs10024642	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10028613	0.91[EUR][1000 genomes]
rs10030586	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10034781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10433970	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10516947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10516950	0.88[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10856908	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10856909	0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs11097406	0.95[ASN][1000 genomes]
rs11097407	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11097411	0.99[ASN][1000 genomes]
rs11097413	0.84[ASN][1000 genomes]
rs11097417	0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs11722476	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11727030	0.89[JPT][hapmap]
rs11943926	0.95[ASN][1000 genomes]
rs12499309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12501138	0.90[ASN][1000 genomes]
rs12505596	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12510326	0.83[ASN][1000 genomes]
rs12511433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12513267	0.93[ASN][1000 genomes]
rs12643901	0.95[ASN][1000 genomes]
rs12645192	0.96[ASN][1000 genomes]
rs12646184	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13108619	0.84[ASN][1000 genomes]
rs13111083	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13112528	1.00[ASN][1000 genomes]
rs13132963	0.97[ASN][1000 genomes]
rs13135934	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13138688	0.81[ASN][1000 genomes]
rs13142645	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13434570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13435702	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17021463	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17302300	0.91[ASN][1000 genomes]
rs17310266	0.98[ASN][1000 genomes]
rs17310526	0.97[ASN][1000 genomes]
rs17374832	0.93[ASN][1000 genomes]
rs17376404	0.99[ASN][1000 genomes]
rs17376488	0.99[ASN][1000 genomes]
rs17623135	0.98[ASN][1000 genomes]
rs183993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876917	0.90[ASN][1000 genomes]
rs1876918	0.91[ASN][1000 genomes]
rs1991316	0.89[JPT][hapmap]
rs2016476	0.88[ASN][1000 genomes]
rs2016483	0.89[ASN][1000 genomes]
rs2059605	0.88[ASN][1000 genomes]
rs2087170	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2129595	0.97[ASN][1000 genomes]
rs2171381	0.99[ASN][1000 genomes]
rs2171384	0.93[ASN][1000 genomes]
rs2276910	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2289186	0.86[ASN][1000 genomes]
rs2632399	0.96[ASN][1000 genomes]
rs2632401	1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2632405	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2632410	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2632411	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2632412	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2632417	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2664871	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2664872	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664880	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664881	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2664892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2664894	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs282447	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs282448	0.91[ASN][1000 genomes]
rs282449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs282450	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28403447	0.87[ASN][1000 genomes]
rs28408270	0.91[ASN][1000 genomes]
rs28469860	0.88[ASN][1000 genomes]
rs2865343	0.93[ASN][1000 genomes]
rs2865344	0.93[ASN][1000 genomes]
rs2865345	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2865350	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2865352	0.84[ASN][1000 genomes]
rs28696050	0.93[ASN][1000 genomes]
rs28701470	0.82[EUR][1000 genomes]
rs28815470	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2883	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28838299	0.80[ASN][1000 genomes]
rs2902979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3106133	0.88[ASN][1000 genomes]
rs3106134	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3106135	0.95[ASN][1000 genomes]
rs3106136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3113862	0.95[ASN][1000 genomes]
rs3113863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34145031	0.98[ASN][1000 genomes]
rs34383543	0.92[ASN][1000 genomes]
rs34396894	0.91[ASN][1000 genomes]
rs34465979	0.88[ASN][1000 genomes]
rs34711938	0.97[ASN][1000 genomes]
rs35361491	0.98[ASN][1000 genomes]
rs35670996	0.98[ASN][1000 genomes]
rs35995707	0.98[ASN][1000 genomes]
rs4235050	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4438731	0.91[ASN][1000 genomes]
rs4558832	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4560373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4692999	0.87[ASN][1000 genomes]
rs4693000	0.87[ASN][1000 genomes]
rs4693003	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4693004	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4693375	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4693376	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs4693377	0.96[ASN][1000 genomes]
rs4693378	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693381	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56197713	0.86[ASN][1000 genomes]
rs60428594	0.91[ASN][1000 genomes]
rs61004493	0.98[ASN][1000 genomes]
rs61069704	0.90[ASN][1000 genomes]
rs61514245	0.98[ASN][1000 genomes]
rs62320439	0.84[ASN][1000 genomes]
rs6532469	0.92[ASN][1000 genomes]
rs6532472	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6532476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66581998	0.96[ASN][1000 genomes]
rs67552174	0.95[ASN][1000 genomes]
rs6817795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6821438	0.91[ASN][1000 genomes]
rs6821638	0.90[ASN][1000 genomes]
rs6823404	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6840674	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6841121	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6855358	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6857967	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6858265	0.91[ASN][1000 genomes]
rs6858342	0.93[ASN][1000 genomes]
rs722486	0.91[ASN][1000 genomes]
rs72665608	0.89[ASN][1000 genomes]
rs72665629	0.93[ASN][1000 genomes]
rs72665658	0.95[ASN][1000 genomes]
rs7435106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7437089	0.84[ASN][1000 genomes]
rs7438414	0.89[JPT][hapmap]
rs7439869	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7442254	0.94[ASN][1000 genomes]
rs7654565	0.93[ASN][1000 genomes]
rs7654919	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7657789	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7669168	0.93[ASN][1000 genomes]
rs767657	0.88[ASN][1000 genomes]
rs7676797	0.82[AFR][1000 genomes]
rs7678054	0.90[ASN][1000 genomes]
rs7680953	0.85[ASN][1000 genomes]
rs7685121	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7697827	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026	1.00[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.98[ASN][1000 genomes]
rs8336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs901615	0.88[ASN][1000 genomes]
rs9307136	0.95[ASN][1000 genomes]
rs9307137	0.93[ASN][1000 genomes]
rs9884209	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9884431	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv1850963	chr4:95146281-95175682	Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11097408	SMARCAD1	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95130000-95176000	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr4:95130200-95193000	Weak transcription	Right Ventricle	heart
3	chr4:95130200-95194000	Weak transcription	Gastric	stomach
4	chr4:95130200-95198200	Weak transcription	Colonic Mucosa	Colon
5	chr4:95131600-95198200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:95131800-95169200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:95136600-95174400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:95138800-95214400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr4:95140200-95167000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:95145400-95175000	Strong transcription	Dnd41	blood
11	chr4:95146000-95214200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr4:95146200-95214200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr4:95146200-95214400	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:95146600-95175800	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr4:95147800-95168400	Strong transcription	Fetal Thymus	thymus
16	chr4:95148000-95169400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:95148200-95180800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr4:95148800-95167000	Weak transcription	Esophagus	oesophagus
19	chr4:95151400-95214400	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr4:95151600-95170400	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr4:95152200-95202000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr4:95152600-95174400	Weak transcription	Brain Angular Gyrus	brain
23	chr4:95153000-95169800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr4:95154200-95173000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:95154600-95168200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr4:95154600-95175800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:95154800-95168200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr4:95155000-95177400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:95155200-95169600	Strong transcription	NH-A	brain
30	chr4:95155400-95169200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr4:95155400-95175800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:95155600-95169200	Strong transcription	Fetal Lung	lung
33	chr4:95155800-95168400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr4:95155800-95169200	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr4:95157400-95168600	Strong transcription	Placenta	Placenta
36	chr4:95157400-95168800	Strong transcription	Adipose Nuclei	Adipose
37	chr4:95157600-95168400	Strong transcription	Osteobl	bone
38	chr4:95157600-95168600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:95157600-95168800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr4:95157600-95172800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr4:95158000-95167800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr4:95158000-95169400	Strong transcription	Liver	Liver
43	chr4:95158000-95172600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:95158200-95168800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:95158200-95173800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:95158200-95225800	Weak transcription	Stomach Mucosa	stomach
47	chr4:95158600-95172600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:95159000-95168600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:95159200-95169600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:95159400-95168600	Strong transcription	Duodenum Mucosa	Duodenum

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