Variant report

Variant	rs2097942
Chromosome Location	chr7:104725105-104725106
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	chr7:104719158..104720755-chr7:104724452..104726723,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1010340	0.81[CEU][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap]
rs1011468	0.81[EUR][1000 genomes]
rs10228174	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10247691	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10252714	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10263499	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1029596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11978288	0.89[EUR][1000 genomes]
rs11981882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12154942	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs12532134	0.92[CEU][hapmap]
rs12532188	0.92[CEU][hapmap]
rs12534212	0.88[EUR][1000 genomes]
rs12537196	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12538590	0.84[CEU][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap]
rs12705296	0.90[EUR][1000 genomes]
rs1468359	0.84[CEU][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap]
rs1558048	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17640472	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs17640508	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.82[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs17640599	0.92[CEU][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs17640623	0.84[CEU][hapmap]
rs17640644	0.84[CEU][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap]
rs17707802	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17707878	0.84[CEU][hapmap]
rs2074753	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2079340	0.92[CEU][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap]
rs2079341	0.84[CEU][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs2106500	0.84[EUR][1000 genomes]
rs2299298	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299305	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2299309	0.84[CEU][hapmap]
rs2299327	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2299328	0.92[CEU][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs3801279	0.84[CEU][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap]
rs4406343	0.92[CEU][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap]
rs4602821	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4727618	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs4730066	0.90[CHD][hapmap]
rs56016333	0.86[ASN][1000 genomes]
rs6466035	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs6466049	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6466051	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap]
rs67665940	0.85[EUR][1000 genomes]
rs68004394	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6945585	0.84[CEU][hapmap]
rs6947388	0.87[EUR][1000 genomes]
rs6949073	0.84[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs6950104	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6950894	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes]
rs6963395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963624	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs6967753	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6972563	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap]
rs6974874	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs6976394	0.88[EUR][1000 genomes]
rs6980244	0.88[EUR][1000 genomes]
rs7776832	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7782673	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7784126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794036	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap]
rs7794285	0.92[CEU][hapmap]
rs7796945	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap]
rs7808226	0.84[CEU][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap]
rs888086	0.88[EUR][1000 genomes]
rs9918494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[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	nsv1029283	chr7:104571741-104729168	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	132 gene(s)	inside rSNPs	diseases
2	nsv888927	chr7:104614664-104781644	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
3	nsv608068	chr7:104622402-104757483	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2097942	CASZ1	trans	parietal	SCAN
rs2097942	COG5	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:104677800-104758200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:104678000-104812200	Strong transcription	Dnd41	blood
3	chr7:104680600-104727000	Strong transcription	Fetal Thymus	thymus
4	chr7:104681200-104758400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr7:104681200-104760400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr7:104681400-104727000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:104685600-104759000	Strong transcription	Primary B cells from peripheral blood	blood
8	chr7:104697000-104726600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:104697600-104726600	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr7:104699800-104738400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:104700800-104726800	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr7:104701200-104727000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:104701400-104758800	Strong transcription	Rectal Mucosa Donor 29	rectum
14	chr7:104701600-104726800	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr7:104701600-104727000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr7:104702200-104727000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr7:104702200-104738200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr7:104702200-104747800	Weak transcription	Stomach Mucosa	stomach
19	chr7:104702800-104758800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:104703200-104725400	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr7:104703200-104727000	Strong transcription	Liver	Liver
22	chr7:104703400-104727400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr7:104703600-104725400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr7:104703600-104727000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:104703600-104759000	Strong transcription	Fetal Intestine Large	intestine
26	chr7:104703800-104725600	Strong transcription	Fetal Lung	lung
27	chr7:104703800-104726200	Strong transcription	Placenta	Placenta
28	chr7:104703800-104726600	Strong transcription	Duodenum Mucosa	Duodenum
29	chr7:104703800-104735400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr7:104704000-104745200	Weak transcription	Psoas Muscle	Psoas
31	chr7:104704600-104727000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr7:104705800-104726800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:104706000-104726400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:104706000-104760200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr7:104707000-104727000	Strong transcription	GM12878-XiMat	blood
36	chr7:104707000-104739200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:104707400-104727000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr7:104707400-104727000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr7:104707800-104726800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr7:104707800-104727000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr7:104707800-104730000	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:104708000-104726800	Strong transcription	Fetal Muscle Trunk	muscle
43	chr7:104709600-104744400	Weak transcription	Right Ventricle	heart
44	chr7:104710600-104726400	Strong transcription	Osteobl	bone
45	chr7:104710600-104727000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr7:104710800-104726600	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr7:104712000-104727000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr7:104712400-104727000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr7:104712400-104758800	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr7:104712600-104736600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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