Variant report

Variant	rs35087366
Chromosome Location	chr3:135917197-135917198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr3:135917171-135917707	U2OS	brain:	n/a	n/a
2	POLR2A	chr3:135913300-135917197	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:135914170-135917278	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:135912206..135917353-chr3:135967047..135972220,20	MCF-7	breast:
2	chr3:135871720..135874662-chr3:135916367..135919284,3	MCF-7	breast:
3	chr3:135912324..135920790-chr3:135965276..135971841,24	K562	blood:
4	chr3:135915695..135917970-chr3:135924534..135927537,3	K562	blood:
5	chr3:135916249..135918777-chr3:135964014..135966844,3	K562	blood:
6	chr3:135914663..135917728-chr3:135920669..135925255,5	MCF-7	breast:
7	chr3:135912523..135919453-chr3:135966949..135972062,29	K562	blood:

No data

Variant related genes	Relation type
MSL2	TF binding region
ENSG00000114054	Chromatin interaction
ENSG00000241438	Chromatin interaction
ENSG00000244740	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1145101	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs13059045	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13065565	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes]
rs13071085	0.83[AFR][1000 genomes]
rs17252498	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs34154714	0.83[AFR][1000 genomes]
rs3821445	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs503973	1.00[JPT][hapmap]
rs610860	1.00[JPT][hapmap]
rs61789561	1.00[ASN][1000 genomes]
rs61789562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61789643	0.83[AFR][1000 genomes]
rs6762209	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs696517	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs71336055	0.83[AFR][1000 genomes]
rs7650071	1.00[ASW][hapmap];1.00[MKK][hapmap];0.83[AFR][1000 genomes]
rs8045	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9647335	1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869409	chr3:135649101-136164174	Strong transcription Genic enhancers Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35087366	TMEM22	cis	cerebellum	SCAN
rs35087366	NCK1	cis	parietal	SCAN
rs35087366	MSL2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:135915400-135917400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr3:135915600-135917200	Flanking Active TSS	Dnd41	blood
3	chr3:135916200-135917200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:135916200-135917200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:135916200-135917200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:135916200-135917400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:135916200-135922600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:135916400-135917200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr3:135916400-135917200	Enhancers	Primary B cells from peripheral blood	blood
10	chr3:135916400-135917200	Enhancers	Primary hematopoietic stem cells	blood
11	chr3:135916400-135917200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:135916400-135917200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr3:135916400-135917400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr3:135916400-135917400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:135916400-135917400	Enhancers	Colon Smooth Muscle	Colon
16	chr3:135916600-135917200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:135916600-135917200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:135916600-135917200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr3:135916600-135917200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr3:135916600-135917200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:135916600-135917200	Enhancers	Adipose Nuclei	Adipose
22	chr3:135916600-135917200	Enhancers	Brain Angular Gyrus	brain
23	chr3:135916600-135917200	Enhancers	Brain Anterior Caudate	brain
24	chr3:135916600-135917200	Enhancers	Brain Hippocampus Middle	brain
25	chr3:135916600-135917200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr3:135916600-135917200	Enhancers	Brain Substantia Nigra	brain
27	chr3:135916600-135917200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr3:135916600-135917200	Enhancers	Fetal Intestine Small	intestine
29	chr3:135916600-135917200	Enhancers	Fetal Kidney	kidney
30	chr3:135916600-135917200	Enhancers	Fetal Lung	lung
31	chr3:135916600-135917200	Enhancers	Fetal Thymus	thymus
32	chr3:135916600-135917200	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr3:135916600-135917200	Enhancers	Rectal Smooth Muscle	rectum
34	chr3:135916600-135917200	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:135916600-135917200	Enhancers	Stomach Mucosa	stomach
36	chr3:135916600-135917200	Enhancers	Stomach Smooth Muscle	stomach
37	chr3:135916600-135917200	Enhancers	Thymus	Thymus
38	chr3:135916600-135917200	Enhancers	HUVEC	blood vessel
39	chr3:135916600-135917200	Enhancers	NHDF-Ad	bronchial
40	chr3:135916600-135917400	Enhancers	Primary B cells from cord blood	blood
41	chr3:135916600-135917400	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:135916600-135917400	Enhancers	Fetal Intestine Large	intestine
43	chr3:135916600-135917400	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr3:135916600-135917400	Enhancers	Hela-S3	cervix
45	chr3:135916600-135917600	Enhancers	Liver	Liver
46	chr3:135916800-135917200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr3:135916800-135917200	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr3:135916800-135917200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:135916800-135917200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr3:135916800-135917200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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