Variant report

Variant	rs4775969
Chromosome Location	chr15:52007217-52007218
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	chr15:52005662..52007756-chr15:52028876..52031424,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2622777	0.90[CHB][hapmap]
rs2652594	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs544023	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4775969	SCG3	cis	cerebellum	SCAN
rs4775969	TMOD2	cis	parietal	SCAN
rs4775969	TMOD2	cis	cerebellum	SCAN
rs4775969	KIAA1370	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
4	chr15:51983000-52013200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:51990000-52016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:51992600-52008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:51993600-52016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:51994400-52007400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:51995400-52013200	Weak transcription	Brain Substantia Nigra	brain
13	chr15:51999800-52018200	Weak transcription	Fetal Stomach	stomach
14	chr15:52000000-52013800	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:52000800-52024000	Weak transcription	Gastric	stomach
16	chr15:52001000-52018600	Weak transcription	Pancreas	Pancrea
17	chr15:52001200-52013000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr15:52001600-52012000	Weak transcription	Primary B cells from cord blood	blood
19	chr15:52002400-52013600	Strong transcription	Fetal Brain Female	brain
20	chr15:52002800-52016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:52003400-52013200	Weak transcription	Aorta	Aorta
22	chr15:52004000-52008400	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr15:52004000-52013400	Strong transcription	Brain Germinal Matrix	brain
24	chr15:52004400-52009800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:52004400-52016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr15:52004600-52007400	Weak transcription	Brain Angular Gyrus	brain
27	chr15:52004800-52012600	Weak transcription	Primary T cells from cord blood	blood
28	chr15:52004800-52018600	Weak transcription	Spleen	Spleen
29	chr15:52005200-52009000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr15:52006200-52013000	Weak transcription	Esophagus	oesophagus
31	chr15:52006400-52013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:52006400-52018400	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:52006600-52012000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:52006800-52007600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr15:52006800-52013400	Weak transcription	K562	blood
36	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
37	chr15:52007200-52007600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:52007200-52007800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:52007200-52008000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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