Variant report

Variant	rs1521177
Chromosome Location	chr1:151782130-151782131
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:151782105-151782536	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151763491..151766160-chr1:151779828..151782203,2	MCF-7	breast:
2	chr1:151774351..151777755-chr1:151779800..151782368,3	K562	blood:
3	chr1:151781556..151784373-chr1:151812437..151814375,2	MCF-7	breast:
4	chr1:151761843..151763864-chr1:151779499..151782273,2	MCF-7	breast:
5	chr1:151781396..151783619-chr1:151785148..151786691,2	MCF-7	breast:
6	chr1:151782043..151784964-chr1:151791094..151793186,2	K562	blood:
7	chr1:151686149..151687760-chr1:151781194..151783599,2	K562	blood:

No data

Variant related genes	Relation type
LINGO4	TF binding region
ENSG00000182134	Chromatin interaction
ENSG00000234614	Chromatin interaction
ENSG00000203288	Chromatin interaction
ENSG00000201134	Chromatin interaction
ENSG00000225556	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10494269	0.82[JPT][hapmap]
rs10888435	0.89[JPT][hapmap]

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	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv516369	chr1:151780177-151820324	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1521177	BCL9	cis	cerebellum	SCAN
rs1521177	SETDB1	cis	parietal	SCAN
rs1521177	LINGO4	cis	cerebellum	SCAN
rs1521177	S100A13	cis	cerebellum	SCAN
rs1521177	LYSMD1	cis	parietal	SCAN
rs1521177	TDRKH	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151764200-151787000	Weak transcription	Right Ventricle	heart
2	chr1:151764200-151792800	Weak transcription	Lung	lung
3	chr1:151764600-151787600	Weak transcription	Primary T cells from cord blood	blood
4	chr1:151765400-151784200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:151770800-151787200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr1:151773200-151784800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:151773400-151784800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:151773400-151785000	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:151774600-151787000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:151775800-151783600	Weak transcription	Psoas Muscle	Psoas
11	chr1:151776600-151787200	Weak transcription	Spleen	Spleen
12	chr1:151778400-151786000	Strong transcription	Thymus	Thymus
13	chr1:151778400-151792800	Weak transcription	Left Ventricle	heart
14	chr1:151778600-151792000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:151778600-151802400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:151778800-151782600	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr1:151778800-151789200	Weak transcription	Fetal Intestine Small	intestine
18	chr1:151779000-151787000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr1:151779200-151783800	Strong transcription	Liver	Liver
20	chr1:151779400-151783000	Enhancers	Brain Cingulate Gyrus	brain
21	chr1:151779400-151784200	Enhancers	Brain Hippocampus Middle	brain
22	chr1:151780000-151793400	Weak transcription	Stomach Mucosa	stomach
23	chr1:151780200-151785400	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr1:151780200-151786800	Weak transcription	Gastric	stomach
25	chr1:151780600-151783600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:151780800-151782600	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr1:151780800-151785400	Weak transcription	Dnd41	blood
28	chr1:151780800-151786600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:151781000-151782200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:151781000-151786000	Strong transcription	Fetal Thymus	thymus
31	chr1:151781200-151782200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:151781400-151783000	Enhancers	Placenta	Placenta
33	chr1:151781600-151783200	Enhancers	Brain Anterior Caudate	brain
34	chr1:151781600-151783600	Weak transcription	Pancreas	Pancrea
35	chr1:151781600-151784000	Enhancers	Brain Substantia Nigra	brain
36	chr1:151781600-151784200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:151781800-151782200	Enhancers	Esophagus	oesophagus
38	chr1:151781800-151782600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr1:151781800-151782600	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:151781800-151783600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr1:151781800-151783600	Enhancers	Hela-S3	cervix
42	chr1:151781800-151787600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:151781800-151788400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:151782000-151782200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:151782000-151782400	Enhancers	Brain Germinal Matrix	brain
46	chr1:151782000-151782600	Enhancers	H1 Cell Line	embryonic stem cell
47	chr1:151782000-151782600	Enhancers	H9 Cell Line	embryonic stem cell
48	chr1:151782000-151782600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:151782000-151782600	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr1:151782000-151782600	Enhancers	Adipose Nuclei	Adipose

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