Variant report

Variant	rs11604399
Chromosome Location	chr11:93225487-93225488
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:93225464..93227548-chr11:93228029..93230930,2	MCF-7	breast:
2	chr11:93225163..93228143-chr15:84362432..84365249,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156218	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs11020387	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11020388	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11020390	0.87[EUR][1000 genomes]
rs11603107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603540	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11603560	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11606505	0.87[EUR][1000 genomes]
rs11607585	0.87[EUR][1000 genomes]
rs12789912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12790221	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12791489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12795164	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12796609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12797006	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12806700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12808363	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12808921	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305660	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2305661	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2605596	0.87[ASN][1000 genomes]
rs2658797	0.87[ASN][1000 genomes]
rs28638787	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3207348	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34028949	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34580908	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34716358	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34819559	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34825570	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35061570	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35364744	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35368196	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35423935	0.86[EUR][1000 genomes]
rs35548120	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35901746	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35930354	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3793999	0.93[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3794002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3794007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58462328	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6483248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6483249	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs66464546	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67927069	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7111773	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs7130465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71480681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71480682	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7365	1.00[CHB][hapmap]
rs7928401	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7933953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7945684	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs897555	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs897558	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv1039623	chr11:93141461-93328739	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	esv2760208	chr11:93172673-93266594	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11604399	SMCO4	cis	Whole Blood	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93207000-93239000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr11:93209000-93231400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr11:93209000-93235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:93209200-93229200	Weak transcription	Dnd41	blood
5	chr11:93209600-93229400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr11:93210600-93231600	Weak transcription	A549	lung
7	chr11:93211000-93225800	Weak transcription	Thymus	Thymus
8	chr11:93211000-93253400	Weak transcription	Primary T cells from cord blood	blood
9	chr11:93211600-93243800	Weak transcription	Fetal Thymus	thymus
10	chr11:93212200-93234800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:93212400-93225800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr11:93214800-93234400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:93215600-93225800	Weak transcription	Colonic Mucosa	Colon
14	chr11:93215600-93226000	Weak transcription	Stomach Mucosa	stomach
15	chr11:93216600-93228600	Enhancers	Liver	Liver
16	chr11:93217200-93226000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr11:93218600-93254400	Weak transcription	Hela-S3	cervix
18	chr11:93218800-93231800	Weak transcription	Ovary	ovary
19	chr11:93218800-93238200	Weak transcription	Esophagus	oesophagus
20	chr11:93218800-93245800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr11:93219400-93225800	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr11:93219800-93227600	Weak transcription	Right Ventricle	heart
23	chr11:93220200-93225600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr11:93220200-93228800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr11:93220600-93230600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:93220600-93230800	Weak transcription	Colon Smooth Muscle	Colon
27	chr11:93220600-93232000	Weak transcription	Left Ventricle	heart
28	chr11:93220800-93226400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:93220800-93227800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:93220800-93235400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr11:93221000-93225600	Enhancers	HepG2	liver
32	chr11:93221200-93228000	Weak transcription	HSMMtube	muscle
33	chr11:93221800-93226000	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr11:93222000-93231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:93222200-93232000	Weak transcription	Spleen	Spleen
36	chr11:93222400-93226400	Weak transcription	Gastric	stomach
37	chr11:93222400-93227200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr11:93222400-93238000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr11:93222800-93225600	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr11:93222800-93225800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:93222800-93225800	Weak transcription	Lung	lung
42	chr11:93222800-93226200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr11:93222800-93231800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr11:93222800-93236000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr11:93223000-93225600	Enhancers	H9 Cell Line	embryonic stem cell
46	chr11:93223000-93226000	Enhancers	Stomach Smooth Muscle	stomach
47	chr11:93223000-93226600	Enhancers	Fetal Lung	lung
48	chr11:93223000-93242800	Weak transcription	Adipose Nuclei	Adipose
49	chr11:93223200-93226800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr11:93223200-93227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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