Variant report

Variant	rs11204776
Chromosome Location	chr1:151069884-151069885
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151065188..151067602-chr1:151069192..151070994,2	K562	blood:

Variant related genes	Relation type
ENSG00000143458	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11204770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11204781	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12066452	1.00[CEU][hapmap]
rs12079532	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12082869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12085364	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12089976	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12090604	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12093277	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs267727	1.00[CEU][hapmap]
rs267728	1.00[CEU][hapmap]
rs4970937	0.91[ASN][1000 genomes]
rs59454556	0.91[ASN][1000 genomes]
rs62621412	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7536645	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv872421	chr1:151055670-151098077	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11204776	CDC42SE1	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
2	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
3	chr1:151044200-151070800	Weak transcription	Fetal Lung	lung
4	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
5	chr1:151044400-151079000	Weak transcription	Left Ventricle	heart
6	chr1:151044400-151079600	Weak transcription	Lung	lung
7	chr1:151044400-151090200	Weak transcription	Gastric	stomach
8	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
9	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
10	chr1:151044600-151070000	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr1:151044600-151076000	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:151044600-151080400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:151044600-151080600	Weak transcription	Brain Anterior Caudate	brain
14	chr1:151044600-151081000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:151044800-151070400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:151044800-151079600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:151044800-151080200	Weak transcription	Fetal Brain Female	brain
18	chr1:151044800-151089400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:151045000-151070400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr1:151045000-151079400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:151045000-151080000	Weak transcription	Brain Angular Gyrus	brain
23	chr1:151045000-151080400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:151045200-151081000	Weak transcription	Placenta	Placenta
25	chr1:151045800-151070400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr1:151047200-151090400	Weak transcription	Dnd41	blood
27	chr1:151047400-151090400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:151047600-151075200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:151047800-151079600	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:151047800-151089200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:151052200-151103000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:151054400-151070400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:151056200-151079600	Weak transcription	Primary B cells from cord blood	blood
34	chr1:151057800-151075200	Weak transcription	Psoas Muscle	Psoas
35	chr1:151060600-151090200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:151061400-151079200	Weak transcription	Osteobl	bone
37	chr1:151061800-151070600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr1:151061800-151090400	Weak transcription	Fetal Kidney	kidney
39	chr1:151061800-151105600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:151062000-151079400	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr1:151062200-151088800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr1:151062400-151076000	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr1:151063200-151074200	Weak transcription	Liver	Liver
44	chr1:151063200-151080800	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:151063400-151070200	Weak transcription	Fetal Stomach	stomach
46	chr1:151063400-151070400	Weak transcription	Brain Hippocampus Middle	brain
47	chr1:151063400-151070600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:151063400-151079600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr1:151064200-151079200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr1:151064200-151103400	Weak transcription	Colonic Mucosa	Colon

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