Variant report

Variant	rs11239580
Chromosome Location	chr10:46133468-46133469
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	chr10:46133340..46134958-chr10:46138632..46141400,2	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11239572	1.00[MKK][hapmap]
rs11239573	0.83[CEU][hapmap];1.00[CHB][hapmap];0.83[TSI][hapmap]
rs11239583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12355931	1.00[CHB][hapmap]
rs34257967	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55654107	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55893855	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55895325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61854126	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61855804	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv993428	chr10:45742877-46224333	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv895108	chr10:45878908-46224333	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv895109	chr10:45882741-46210665	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv895112	chr10:46012620-46202216	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1050880	chr10:46091441-46160597	Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv540588	chr10:46091441-46160597	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv947911	chr10:46116371-46136816	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11239580	ZNF485	cis	parietal	SCAN
rs11239580	ANTXRL	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:46090600-46167600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:46096200-46142000	Weak transcription	Brain Anterior Caudate	brain
3	chr10:46098200-46153400	Weak transcription	HSMM	muscle
4	chr10:46100200-46142600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr10:46103400-46142200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr10:46103800-46134600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:46104400-46151400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:46105600-46141600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr10:46106400-46137000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr10:46106400-46141400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr10:46106400-46142000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr10:46106800-46142000	Weak transcription	Fetal Kidney	kidney
13	chr10:46106800-46146400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr10:46107800-46141800	Weak transcription	Colon Smooth Muscle	Colon
15	chr10:46107800-46142000	Weak transcription	Esophagus	oesophagus
16	chr10:46108000-46155800	Weak transcription	Brain Angular Gyrus	brain
17	chr10:46108200-46142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr10:46108400-46142000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:46108400-46149400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:46108400-46167000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr10:46108600-46149200	Weak transcription	Brain Hippocampus Middle	brain
22	chr10:46108600-46155400	Weak transcription	Fetal Intestine Small	intestine
23	chr10:46108800-46142000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr10:46110200-46153800	Weak transcription	NH-A	brain
25	chr10:46110800-46156800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr10:46112200-46152400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr10:46118800-46142400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:46119800-46137000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr10:46119800-46148200	Weak transcription	Colonic Mucosa	Colon
30	chr10:46120000-46157800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr10:46120200-46148400	Weak transcription	Small Intestine	intestine
32	chr10:46122200-46142000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr10:46122200-46154600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr10:46122200-46157200	Weak transcription	Gastric	stomach
35	chr10:46122400-46134000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr10:46122400-46137200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:46122400-46141800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr10:46122400-46142000	Weak transcription	Fetal Lung	lung
39	chr10:46122400-46142200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr10:46122400-46149000	Weak transcription	Brain Substantia Nigra	brain
41	chr10:46122400-46156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr10:46122600-46133600	Weak transcription	Fetal Stomach	stomach
43	chr10:46122600-46133800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:46122600-46136400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr10:46122600-46139400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr10:46122600-46140600	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr10:46122600-46141400	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr10:46122600-46141800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr10:46122600-46142000	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr10:46122600-46142000	Weak transcription	Fetal Muscle Leg	muscle

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