Variant report

Variant	rs7590275
Chromosome Location	chr2:172283513-172283514
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	chr2:172271841..172274486-chr2:172281833..172284953,3	K562	blood:
2	chr2:172282044..172287208-chr2:172288803..172293101,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10460358	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10930473	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11677562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11679641	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12052810	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12465868	0.96[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12469151	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471094	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12616940	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1558963	0.95[JPT][hapmap];1.00[MEX][hapmap]
rs17285260	0.84[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1921776	1.00[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2058927	0.91[ASN][1000 genomes]
rs2356709	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.98[ASN][1000 genomes]
rs4667685	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55862836	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62181358	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62183460	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66893860	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6747400	0.95[JPT][hapmap];1.00[MEX][hapmap]
rs727231	1.00[MEX][hapmap]
rs997666	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]

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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv3349868	chr2:172276494-172302401	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7590275	WIPF1	cis	parietal	SCAN
rs7590275	GAD1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172266400-172289600	Weak transcription	Psoas Muscle	Psoas
3	chr2:172266400-172289600	Weak transcription	Right Ventricle	heart
4	chr2:172268800-172289200	Weak transcription	HSMM	muscle
5	chr2:172272600-172287200	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:172272600-172289000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:172272600-172289400	Weak transcription	HSMMtube	muscle
8	chr2:172273000-172283600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:172278000-172288600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:172278200-172289600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr2:172279200-172284200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:172280600-172287800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:172280600-172289600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr2:172281000-172285000	Weak transcription	Fetal Intestine Large	intestine
15	chr2:172281000-172287200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr2:172281000-172287400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:172281000-172289600	Weak transcription	Left Ventricle	heart
18	chr2:172281000-172289600	Weak transcription	Right Atrium	heart
19	chr2:172281000-172290200	Weak transcription	Aorta	Aorta
20	chr2:172281200-172290000	Weak transcription	Ovary	ovary
21	chr2:172281600-172288000	ZNF genes & repeats	GM12878-XiMat	blood
22	chr2:172281600-172289400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr2:172282000-172287400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:172282200-172283600	Weak transcription	Primary B cells from cord blood	blood
25	chr2:172282200-172283800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:172282200-172286800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:172282200-172287000	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:172282200-172287000	Weak transcription	HMEC	breast
29	chr2:172282200-172287200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:172282200-172287200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:172282200-172287200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:172282200-172287400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr2:172282200-172287400	Weak transcription	Esophagus	oesophagus
34	chr2:172282200-172287600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:172282200-172288400	Weak transcription	Fetal Lung	lung
36	chr2:172282200-172288600	Weak transcription	Fetal Muscle Trunk	muscle
37	chr2:172282200-172288800	Weak transcription	NHLF	lung
38	chr2:172282200-172289200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr2:172282200-172289200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr2:172282400-172284800	Weak transcription	HepG2	liver
41	chr2:172282400-172285400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:172282400-172285800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr2:172282400-172287000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:172282400-172287000	Weak transcription	NHEK	skin
45	chr2:172282400-172287200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:172282400-172287600	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:172282400-172287600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr2:172282400-172287600	Weak transcription	A549	lung
49	chr2:172283000-172287200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:172283400-172283600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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