Variant report

Variant	rs11800843
Chromosome Location	chr1:169339031-169339032
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169337822..169339719-chr1:169451874..169454199,3	K562	blood:
2	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
3	chr1:169338121..169342264-chr1:169451874..169455112,4	K562	blood:
4	chr1:169337259..169338842-chr1:169338923..169340546,3	MCF-7	breast:
5	chr1:169338197..169339910-chr1:169345261..169347920,2	MCF-7	breast:
6	chr1:169275275..169277238-chr1:169338409..169341241,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction
ENSG00000117475	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10158131	0.82[CEU][hapmap];0.86[MEX][hapmap]
rs10458395	0.81[ASN][1000 genomes]
rs10458396	0.81[ASN][1000 genomes]
rs10458397	0.81[ASN][1000 genomes]
rs10489187	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489188	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800439	0.86[CHB][hapmap]
rs10800441	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs10800446	0.81[ASN][1000 genomes]
rs10919140	0.86[MEX][hapmap]
rs10919146	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10919155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919163	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919164	0.81[ASN][1000 genomes]
rs10919167	0.81[ASN][1000 genomes]
rs1112839	0.81[ASN][1000 genomes]
rs11799936	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11799948	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808015	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11808274	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs11809378	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12021770	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023025	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023117	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023892	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12024897	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs12026287	0.81[ASN][1000 genomes]
rs12026728	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026996	0.80[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12028813	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12029853	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12030320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12034986	0.81[ASN][1000 genomes]
rs12037211	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs12038609	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs12039443	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12043489	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs12045202	0.82[YRI][hapmap]
rs12046139	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs12049227	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12239720	0.84[ASN][1000 genomes]
rs12563090	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs12564884	0.81[ASN][1000 genomes]
rs1400838	1.00[CEU][hapmap];0.89[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1415928	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1589113	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16828170	0.89[JPT][hapmap];0.83[YRI][hapmap]
rs16862118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862172	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862199	0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1980198	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2003652	0.81[ASN][1000 genomes]
rs2003654	0.80[ASN][1000 genomes]
rs2014061	0.81[ASN][1000 genomes]
rs2235195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2268048	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[YRI][hapmap]
rs2275299	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs28566091	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35269183	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737682	0.85[CHB][hapmap]
rs3753303	0.81[ASN][1000 genomes]
rs3766089	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.84[YRI][hapmap]
rs3766096	0.81[ASN][1000 genomes]
rs3818844	0.86[CHB][hapmap]
rs4656670	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs56859218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61807018	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808977	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808978	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808980	0.84[ASN][1000 genomes]
rs6427186	0.81[ASN][1000 genomes]
rs6427191	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656923	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6660945	0.81[ASN][1000 genomes]
rs6669741	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs6677410	0.86[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs6690801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696428	0.81[ASN][1000 genomes]
rs6696810	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs72702156	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72702179	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72702188	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528375	0.81[ASN][1000 genomes]
rs7528449	0.81[ASN][1000 genomes]
rs7534737	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs7535788	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7539415	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs7554703	1.00[ASN][1000 genomes]
rs9633334	0.90[ASW][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.84[YRI][hapmap]
rs9659035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988604	0.90[ASW][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11800843	F5	cis	cerebellum	SCAN
rs11800843	C1orf114	cis	cerebellum	SCAN
rs11800843	NME7	cis	parietal	SCAN
rs11800843	SCYL3	cis	parietal	SCAN
rs11800843	C1orf114	cis	parietal	SCAN
rs11800843	FMO9P	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169336200-169339200	Active TSS	HMEC	breast
2	chr1:169338000-169339200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:169338000-169340000	Weak transcription	Left Ventricle	heart
4	chr1:169338000-169351200	Weak transcription	Lung	lung
5	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
6	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
7	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
8	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
9	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:169338000-169365200	Weak transcription	Gastric	stomach
11	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
12	chr1:169338200-169339200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr1:169338200-169339200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:169338200-169339200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:169338200-169339400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:169338200-169339400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:169338200-169340600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:169338200-169341200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:169338200-169341600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:169338200-169345800	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:169338200-169345800	Weak transcription	Ovary	ovary
22	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
28	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:169338400-169339200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:169338400-169339200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr1:169338400-169339200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr1:169338400-169339200	Enhancers	Fetal Brain Male	brain
33	chr1:169338400-169339200	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:169338400-169345800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:169338400-169345800	Weak transcription	Right Ventricle	heart
36	chr1:169338400-169349600	Weak transcription	HSMMtube	muscle
37	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr1:169338600-169339200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:169338600-169339200	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr1:169338600-169339200	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr1:169338600-169339200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr1:169338600-169339200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:169338600-169339200	Weak transcription	Brain Germinal Matrix	brain
45	chr1:169338600-169339200	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:169338600-169339200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr1:169338600-169339200	Weak transcription	Fetal Thymus	thymus
48	chr1:169338600-169339200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr1:169338600-169339200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:169338600-169339200	Weak transcription	Rectal Smooth Muscle	rectum

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