Variant report

Variant	rs7021679
Chromosome Location	chr9:92766404-92766405
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	chr9:92217272..92218834-chr9:92763919..92766631,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10117261	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs10118552	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10120740	0.84[ASN][1000 genomes]
rs10123198	0.80[ASN][1000 genomes]
rs10821386	0.80[CHB][hapmap]
rs10821471	0.84[MKK][hapmap]
rs10821475	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap]
rs10821501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821505	0.81[AFR][1000 genomes]
rs10821512	0.82[AFR][1000 genomes]
rs10993333	0.86[CHB][hapmap]
rs10993656	0.85[YRI][hapmap]
rs10993699	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1348383	0.82[AFR][1000 genomes]
rs1443364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1999100	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4744020	0.80[MKK][hapmap]
rs496129	0.86[AFR][1000 genomes]
rs586750	0.81[AFR][1000 genomes]
rs601472	0.81[ASW][hapmap]
rs633926	0.81[ASW][hapmap]
rs6479580	0.81[ASN][1000 genomes]
rs652454	0.88[ASW][hapmap];0.85[CEU][hapmap];0.87[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.87[AFR][1000 genomes]
rs657899	0.87[ASW][hapmap];0.85[CEU][hapmap];0.87[GIH][hapmap];0.84[LWK][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap]
rs661741	0.84[AFR][1000 genomes]
rs679273	0.81[ASW][hapmap]
rs7038428	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs721833	0.81[ASN][1000 genomes]
rs7866392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7874166	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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	nsv893561	chr9:92732368-92802101	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv482303	chr9:92752928-92890226	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7021679	ROR2	cis	parietal	SCAN
rs7021679	SYK	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:92757400-92770000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:92757600-92770000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:92758800-92767600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:92761200-92767400	Enhancers	Fetal Muscle Leg	muscle
5	chr9:92761800-92766600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr9:92762400-92766600	Enhancers	Colon Smooth Muscle	Colon
7	chr9:92762600-92766600	Enhancers	HSMMtube	muscle
8	chr9:92762600-92769600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr9:92762800-92769600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:92763000-92766600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr9:92763000-92766600	Enhancers	Left Ventricle	heart
12	chr9:92763000-92766600	Enhancers	Pancreas	Pancrea
13	chr9:92763000-92766600	Enhancers	Rectal Smooth Muscle	rectum
14	chr9:92763000-92766800	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr9:92763000-92768000	Enhancers	Ovary	ovary
16	chr9:92763400-92767200	Weak transcription	Primary B cells from cord blood	blood
17	chr9:92763600-92769800	Weak transcription	Gastric	stomach
18	chr9:92763600-92769800	Weak transcription	NHDF-Ad	bronchial
19	chr9:92763800-92766600	Enhancers	Fetal Muscle Trunk	muscle
20	chr9:92764200-92766600	Enhancers	Fetal Brain Female	brain
21	chr9:92764200-92771200	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr9:92764600-92766600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:92764800-92769800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr9:92765000-92769800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr9:92765000-92770000	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr9:92765000-92770400	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr9:92765200-92767000	Enhancers	Brain Germinal Matrix	brain
28	chr9:92765200-92767200	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr9:92765200-92767600	Weak transcription	Placenta	Placenta
30	chr9:92765200-92769800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:92765200-92771400	Weak transcription	Colonic Mucosa	Colon
32	chr9:92765400-92767600	Weak transcription	Fetal Intestine Small	intestine
33	chr9:92765400-92769000	Weak transcription	Stomach Mucosa	stomach
34	chr9:92765400-92769400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:92765400-92769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:92765400-92769800	Weak transcription	Fetal Intestine Large	intestine
37	chr9:92765600-92766600	Weak transcription	Brain Angular Gyrus	brain
38	chr9:92765600-92766800	Enhancers	Brain Hippocampus Middle	brain
39	chr9:92765800-92766600	Enhancers	Aorta	Aorta
40	chr9:92765800-92767000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr9:92765800-92767000	Weak transcription	Fetal Lung	lung
42	chr9:92765800-92767000	Enhancers	Stomach Smooth Muscle	stomach
43	chr9:92765800-92775200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr9:92766000-92766600	Enhancers	Brain Anterior Caudate	brain
45	chr9:92766000-92766600	Enhancers	Psoas Muscle	Psoas
46	chr9:92766000-92766600	Enhancers	Right Atrium	heart
47	chr9:92766200-92766600	Enhancers	Esophagus	oesophagus
48	chr9:92766200-92766600	Enhancers	Right Ventricle	heart
49	chr9:92766200-92769200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:92766400-92766600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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