Variant report

Variant	rs3180196
Chromosome Location	chr6:13801615-13801616
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	chr6:13800692..13802953-chr6:13824224..13826092,2	K562	blood:

Variant related genes	Relation type
ENSG00000272209	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2071835	1.00[MKK][hapmap]
rs9349797	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9382303	1.00[MKK][hapmap]

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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3180196	CCDC90A	cis	parietal	SCAN
rs3180196	CCDC90A	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13766800-13802400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:13781000-13802000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr6:13788000-13802600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr6:13788000-13810600	Weak transcription	Fetal Heart	heart
5	chr6:13788000-13810800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:13788000-13812200	Weak transcription	Aorta	Aorta
7	chr6:13788000-13813200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:13788000-13813400	Weak transcription	Brain Germinal Matrix	brain
9	chr6:13788200-13807600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr6:13788400-13810600	Weak transcription	Colonic Mucosa	Colon
11	chr6:13788600-13810800	Weak transcription	Stomach Mucosa	stomach
12	chr6:13788800-13810600	Weak transcription	Small Intestine	intestine
13	chr6:13788800-13812200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr6:13788800-13813600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr6:13789600-13803800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:13792400-13802600	Weak transcription	Pancreas	Pancrea
17	chr6:13792600-13810800	Weak transcription	Spleen	Spleen
18	chr6:13793000-13813200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr6:13794800-13812200	Weak transcription	HMEC	breast
20	chr6:13795200-13808200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:13795200-13810800	Weak transcription	NHLF	lung
22	chr6:13795400-13812200	Weak transcription	HUVEC	blood vessel
23	chr6:13795800-13803000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr6:13796000-13805600	Weak transcription	NH-A	brain
25	chr6:13796000-13809800	Strong transcription	Dnd41	blood
26	chr6:13796000-13811000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:13796400-13803800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:13796400-13807600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:13796800-13803200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:13796800-13803600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:13796800-13809800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:13797000-13802600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr6:13797000-13802800	Strong transcription	Adipose Nuclei	Adipose
34	chr6:13797000-13803000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr6:13797000-13803200	Strong transcription	Liver	Liver
36	chr6:13797000-13807000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:13797000-13807400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr6:13797000-13807600	Strong transcription	Fetal Thymus	thymus
39	chr6:13797000-13809800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr6:13797200-13802800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:13797200-13806400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr6:13797600-13803000	Strong transcription	Lung	lung
43	chr6:13797600-13803400	Strong transcription	Primary T cells from cord blood	blood
44	chr6:13797600-13807400	Strong transcription	Fetal Stomach	stomach
45	chr6:13797600-13808200	Weak transcription	HSMM	muscle
46	chr6:13797600-13810600	Strong transcription	Fetal Intestine Small	intestine
47	chr6:13797800-13807400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:13798400-13802800	Strong transcription	Brain Cingulate Gyrus	brain
49	chr6:13798400-13803000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:13798400-13807400	Strong transcription	Fetal Intestine Large	intestine

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