Variant report

Variant	rs2286680
Chromosome Location	chr7:6035507-6035508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6034265..6036958-chr7:6048918..6052567,3	K562	blood:
2	chr7:6034265..6036958-chr7:6048881..6052567,3	K562	blood:
3	chr7:6035383..6037045-chr7:6343734..6346245,2	MCF-7	breast:
4	chr7:6035426..6037082-chr7:6372151..6373884,2	MCF-7	breast:
5	chr7:6034085..6036991-chr7:6144638..6147451,2	MCF-7	breast:
6	chr7:6033194..6036666-chr7:6097186..6100537,4	MCF-7	breast:
7	chr7:6029549..6032323-chr7:6033802..6035635,3	MCF-7	breast:
8	chr7:6028083..6031843-chr7:6035070..6038579,3	K562	blood:

Variant related genes	Relation type
ENSG00000106346	Chromatin interaction
ENSG00000106305	Chromatin interaction
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10249759	0.81[JPT][hapmap]
rs10254125	0.90[JPT][hapmap]
rs1062372	0.88[TSI][hapmap]
rs11770056	0.81[JPT][hapmap]
rs11770075	0.81[JPT][hapmap]
rs12112229	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12702460	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702461	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702463	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12702464	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12702468	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13240138	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13245536	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13311041	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1860462	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1986625	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2009115	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302332	0.81[JPT][hapmap]
rs34197105	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3735295	0.95[TSI][hapmap]
rs3735296	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3779107	0.88[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3779109	0.83[AFR][1000 genomes]
rs525090	0.81[JPT][hapmap]
rs59901370	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6463525	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6463527	0.81[JPT][hapmap]
rs6949598	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6964944	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6973250	0.85[CEU][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap]
rs6974270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979676	0.83[MKK][hapmap]
rs71524066	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7781199	0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs7788051	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7793254	0.85[ASN][1000 genomes]
rs7799214	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7805798	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 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	nsv933765	chr7:6029095-6039048	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	nsv933445	chr7:6034999-6039048	Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
20	nsv605998	chr7:6035065-6102034	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2286680	PMS2	cis	cerebellum	SCAN
rs2286680	PMS2	cis	parietal	SCAN
rs2286680	KIAA0415	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6010400-6048000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:6016200-6047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:6017400-6038600	Weak transcription	Brain Angular Gyrus	brain
4	chr7:6022600-6048000	Weak transcription	NHLF	lung
5	chr7:6025000-6039600	Weak transcription	Esophagus	oesophagus
6	chr7:6025000-6048000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:6025200-6046800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr7:6025800-6038600	Weak transcription	Aorta	Aorta
9	chr7:6025800-6045200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr7:6026200-6042800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:6026200-6045400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:6026200-6046200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:6026400-6036000	Strong transcription	Adipose Nuclei	Adipose
14	chr7:6026400-6036800	Strong transcription	Liver	Liver
15	chr7:6026400-6037200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr7:6026400-6040000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr7:6026400-6042000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:6026400-6043600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr7:6026400-6043600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:6026400-6043600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr7:6026400-6044000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr7:6026400-6044000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr7:6026400-6045000	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr7:6026400-6045000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:6026400-6045400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:6026400-6045600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:6026600-6042800	Strong transcription	Fetal Stomach	stomach
28	chr7:6026600-6045400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr7:6027600-6047200	Weak transcription	Fetal Kidney	kidney
30	chr7:6028000-6048000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr7:6028200-6045000	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr7:6029000-6048000	Weak transcription	Right Ventricle	heart
33	chr7:6029400-6037800	Weak transcription	Lung	lung
34	chr7:6029600-6047000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr7:6030800-6039800	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr7:6031400-6036000	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr7:6031600-6040200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr7:6032200-6037600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:6032200-6042400	Strong transcription	Fetal Intestine Small	intestine
40	chr7:6032200-6045400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr7:6032800-6040200	Strong transcription	Primary T cells from cord blood	blood
42	chr7:6033000-6036600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr7:6033200-6036200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr7:6033200-6036200	Strong transcription	Fetal Intestine Large	intestine
45	chr7:6033200-6040600	Strong transcription	Spleen	Spleen
46	chr7:6033400-6040000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr7:6033400-6043800	Strong transcription	Primary B cells from peripheral blood	blood
48	chr7:6033600-6035800	Strong transcription	HUVEC	blood vessel
49	chr7:6033600-6036000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr7:6033600-6036000	Strong transcription	Brain Hippocampus Middle	brain

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