Variant report

Variant	rs2228006
Chromosome Location	chr7:6026775-6026776
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12538339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1805319	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2079819	0.85[ASN][1000 genomes]
rs3801032	0.81[CHD][hapmap];0.94[MEX][hapmap];0.83[AMR][1000 genomes]
rs3857757	0.83[AMR][1000 genomes]
rs4720658	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4724768	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4724770	0.81[CHD][hapmap];0.94[MEX][hapmap];0.84[AMR][1000 genomes]
rs475323	0.88[MEX][hapmap];0.83[AMR][1000 genomes]
rs523276	0.84[AMR][1000 genomes]
rs540208	0.82[AMR][1000 genomes]
rs6954766	0.82[ASN][1000 genomes]
rs6976251	0.85[AMR][1000 genomes]
rs7384784	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7803611	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
2	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
3	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
5	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
6	nsv1034215	chr7:5748982-6056619	Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv1016690	chr7:5749222-6056619	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
8	nsv1027679	chr7:5760731-6056619	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
10	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
11	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
12	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
13	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription 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	127 gene(s)	inside rSNPs	diseases
14	nsv433017	chr7:5853557-6045391	Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv830894	chr7:5889658-6072215	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
16	nsv1034916	chr7:5934780-6158970	Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
17	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
18	nsv970789	chr7:5958445-6027048	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2228006	CCZ1	cis	lymphoblastoid	seeQTL
rs2228006	C7orf28B	cis	lymphoblastoid	seeQTL
rs2228006	FBXL18	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6010200-6026800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:6010400-6028600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:6010400-6048000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr7:6012400-6028800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:6014600-6027200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr7:6015200-6028600	Weak transcription	Gastric	stomach
7	chr7:6015800-6033600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:6016000-6028600	Weak transcription	Brain Substantia Nigra	brain
9	chr7:6016200-6026800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr7:6016200-6027800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:6016200-6028800	Weak transcription	Fetal Lung	lung
12	chr7:6016200-6029400	Weak transcription	A549	lung
13	chr7:6016200-6029400	Weak transcription	Hela-S3	cervix
14	chr7:6016200-6047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:6016600-6033800	Weak transcription	GM12878-XiMat	blood
16	chr7:6017000-6026800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr7:6017000-6035000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:6017400-6038600	Weak transcription	Brain Angular Gyrus	brain
19	chr7:6017600-6028000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr7:6017800-6028600	Weak transcription	Brain Hippocampus Middle	brain
21	chr7:6017800-6030200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr7:6018000-6028600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr7:6018000-6033600	Weak transcription	HUVEC	blood vessel
24	chr7:6018200-6034400	Weak transcription	K562	blood
25	chr7:6018200-6035000	Weak transcription	NH-A	brain
26	chr7:6018400-6035400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr7:6018800-6026800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:6018800-6027800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr7:6019000-6028000	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr7:6019200-6026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:6019200-6028600	Weak transcription	Left Ventricle	heart
32	chr7:6019400-6035400	Weak transcription	HepG2	liver
33	chr7:6019600-6030200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:6019600-6035200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr7:6019600-6035200	Weak transcription	Fetal Brain Male	brain
36	chr7:6020000-6027800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr7:6021600-6028200	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr7:6022600-6026800	Weak transcription	Thymus	Thymus
39	chr7:6022600-6048000	Weak transcription	NHLF	lung
40	chr7:6023400-6029000	Weak transcription	NHEK	skin
41	chr7:6023600-6035000	Weak transcription	HSMMtube	muscle
42	chr7:6024800-6029200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr7:6024800-6033200	Weak transcription	Small Intestine	intestine
44	chr7:6025000-6028000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr7:6025000-6035400	Weak transcription	Psoas Muscle	Psoas
46	chr7:6025000-6039600	Weak transcription	Esophagus	oesophagus
47	chr7:6025000-6048000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr7:6025200-6026800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr7:6025200-6026800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr7:6025200-6035000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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