Variant report

Variant	rs9498262
Chromosome Location	chr6:149556161-149556162
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149353437..149355282-chr6:149555102..149556792,2	MCF-7	breast:
2	chr6:149544065..149545695-chr6:149554357..149556733,2	K562	blood:
3	chr6:149555445..149557100-chr6:149637595..149639375,2	K562	blood:
4	chr6:149544065..149546954-chr6:149554614..149556733,2	K562	blood:
5	chr6:149553886..149556657-chr6:149559503..149563142,3	K562	blood:

Variant related genes	Relation type
ENSG00000236591	Chromatin interaction
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11966037	0.84[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs12191351	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4897095	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4897096	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6570954	0.85[ASN][1000 genomes]
rs6900499	0.85[ASN][1000 genomes]
rs6935536	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6937702	0.85[ASN][1000 genomes]
rs7748981	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs926408	0.83[CHB][hapmap];0.82[GIH][hapmap];0.81[EUR][1000 genomes]
rs9377199	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9390663	0.88[CHB][hapmap];0.94[JPT][hapmap]
rs9485360	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9485361	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9485362	0.83[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9498266	0.84[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[AMR][1000 genomes];0.85[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	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9498262	RAET1L	cis	cerebellum	SCAN
rs9498262	LATS1	cis	parietal	SCAN
rs9498262	RAET1L	cis	parietal	SCAN
rs9498262	TAB2	cis	intralobular white matter	BrainEAC
rs9498262	TAB2	cis	brain	BrainEAC

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149542200-149560600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr6:149545800-149557800	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:149545800-149560200	Weak transcription	Right Atrium	heart
4	chr6:149546800-149556200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:149549600-149557200	Weak transcription	Fetal Stomach	stomach
6	chr6:149550200-149557800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:149551000-149557600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr6:149551600-149556400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr6:149551800-149558000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr6:149552000-149556400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:149552400-149556800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:149552600-149556600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:149552800-149556800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr6:149553000-149557000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr6:149553000-149557000	Enhancers	Fetal Thymus	thymus
16	chr6:149553200-149556800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr6:149553400-149557200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr6:149553600-149557000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:149553600-149557000	Enhancers	HMEC	breast
20	chr6:149553800-149556600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:149553800-149558200	Enhancers	HUVEC	blood vessel
22	chr6:149554000-149556600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:149554000-149557000	Enhancers	HSMM	muscle
24	chr6:149554000-149557200	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr6:149554000-149558200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:149554200-149556800	Weak transcription	Fetal Muscle Leg	muscle
27	chr6:149554200-149556800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr6:149554200-149558000	Weak transcription	Brain Anterior Caudate	brain
29	chr6:149554400-149556800	Enhancers	Muscle Satellite Cultured Cells	--
30	chr6:149554400-149556800	Weak transcription	Brain Substantia Nigra	brain
31	chr6:149554400-149557400	Weak transcription	Fetal Heart	heart
32	chr6:149554600-149556600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:149554600-149557400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:149555000-149556200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:149555000-149557400	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:149555200-149556400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr6:149555200-149557000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:149555200-149557000	Enhancers	Fetal Lung	lung
39	chr6:149555200-149557000	Enhancers	Ovary	ovary
40	chr6:149555200-149557000	Enhancers	Pancreas	Pancrea
41	chr6:149555200-149557200	Enhancers	Osteobl	bone
42	chr6:149555200-149557400	Enhancers	Primary hematopoietic stem cells	blood
43	chr6:149555400-149556200	Flanking Active TSS	NH-A	brain
44	chr6:149555400-149556800	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr6:149555400-149557200	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr6:149555600-149556200	Enhancers	HepG2	liver
47	chr6:149555600-149556600	Enhancers	A549	lung
48	chr6:149555600-149557400	Enhancers	Primary B cells from peripheral blood	blood
49	chr6:149555600-149562200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:149555800-149556200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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