Variant report

Variant	rs7022455
Chromosome Location	chr9:100866872-100866873
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59915399..59917132-chr9:100865983..100868318,2	MCF-7	breast:
2	chr9:100861454..100863501-chr9:100865367..100867490,2	MCF-7	breast:
3	chr9:100865961..100868897-chr9:100875426..100877165,2	MCF-7	breast:
4	chr9:100865376..100868283-chr9:100880177..100883059,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000106785	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10985048	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10985065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12552242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16912622	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs2281732	0.82[JPT][hapmap]
rs4742716	0.82[JPT][hapmap]
rs4743157	0.82[JPT][hapmap]
rs4743158	0.82[JPT][hapmap]
rs4743164	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55972150	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6478539	0.86[CHD][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap]
rs6478556	0.80[GIH][hapmap];0.82[JPT][hapmap]
rs6478563	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7852752	0.83[CEU][hapmap]
rs7855251	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7865340	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7869762	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1040483	chr9:100835325-100868437	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
3	nsv614935	chr9:100861387-100876284	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7022455	PHF2	cis	parietal	SCAN
rs7022455	NANS	cis	parietal	SCAN
rs7022455	ZNF169	cis	cerebellum	SCAN
rs7022455	C9orf156	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100847400-100869400	Weak transcription	A549	lung
2	chr9:100847600-100867000	Weak transcription	Hela-S3	cervix
3	chr9:100850400-100868000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:100850400-100880400	Weak transcription	HSMM	muscle
5	chr9:100850600-100875400	Weak transcription	NHLF	lung
6	chr9:100850600-100880600	Weak transcription	Fetal Lung	lung
7	chr9:100854600-100870800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:100854800-100870800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:100855000-100868200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:100857800-100869400	Weak transcription	Left Ventricle	heart
11	chr9:100858200-100868000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:100858200-100869000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr9:100858400-100872000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:100858600-100880400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:100858600-100880400	Weak transcription	Brain Anterior Caudate	brain
16	chr9:100858800-100867000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:100859000-100867000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr9:100859200-100880600	Weak transcription	Gastric	stomach
19	chr9:100860000-100869000	Strong transcription	Fetal Intestine Small	intestine
20	chr9:100860200-100880800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:100860600-100868000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:100861400-100868000	Enhancers	Primary hematopoietic stem cells	blood
23	chr9:100861400-100871800	Enhancers	Primary B cells from peripheral blood	blood
24	chr9:100861400-100880600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:100862200-100872200	Enhancers	Primary B cells from cord blood	blood
26	chr9:100862200-100872400	Weak transcription	Esophagus	oesophagus
27	chr9:100862400-100867000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:100862400-100867000	Weak transcription	Spleen	Spleen
29	chr9:100862400-100867200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr9:100862400-100867200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr9:100862400-100867200	Weak transcription	Lung	lung
32	chr9:100862400-100869000	Weak transcription	K562	blood
33	chr9:100862400-100869600	Weak transcription	Adipose Nuclei	Adipose
34	chr9:100862400-100871800	Weak transcription	HMEC	breast
35	chr9:100862400-100880000	Weak transcription	Small Intestine	intestine
36	chr9:100862400-100880600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr9:100862600-100869000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:100862800-100867000	Weak transcription	Colonic Mucosa	Colon
39	chr9:100864000-100867200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:100864000-100867800	Weak transcription	Fetal Muscle Leg	muscle
41	chr9:100864200-100867400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr9:100864600-100867200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr9:100864600-100871000	Weak transcription	NHEK	skin
44	chr9:100864600-100880400	Weak transcription	Brain Hippocampus Middle	brain
45	chr9:100864600-100880800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:100864800-100867000	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr9:100864800-100868000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:100864800-100869000	Weak transcription	Brain Germinal Matrix	brain
49	chr9:100864800-100869200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr9:100864800-100869600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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