Variant report

Variant	rs2009115
Chromosome Location	chr7:6052556-6052557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr7:6052335-6052733	HepG2	liver:	n/a	n/a
2	ELF1	chr7:6052378-6052702	HepG2	liver:	n/a	n/a
3	FOXA1	chr7:6052321-6052732	HepG2	liver:	n/a	n/a
4	FOXA2	chr7:6052424-6052803	HepG2	liver:	n/a	n/a
5	TCF7L2	chr7:6051988-6052636	HepG2	liver:	n/a	n/a
6	ELF1	chr7:6052347-6052713	HepG2	liver:	n/a	n/a
7	POLR2A	chr7:6051221-6053738	HepG2	liver:	n/a	n/a
8	FOXA1	chr7:6052332-6052848	HepG2	liver:	n/a	n/a
9	MAFK	chr7:6052430-6052791	HepG2	liver:	n/a	chr7:6052595-6052610
10	GATA3	chr7:6052363-6052940	MCF-7	breast:	n/a	n/a
11	CEBPB	chr7:6052079-6052735	HepG2	liver:	n/a	chr7:6052244-6052255
12	FOXA1	chr7:6052445-6052780	T-47D	breast:	n/a	n/a
13	TCF7L2	chr7:6052402-6052694	MCF-7	breast:	n/a	n/a
14	POLR2A	chr7:6052318-6052840	HepG2	liver:	n/a	n/a
15	POLR2A	chr7:6052159-6052806	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr7:6051902-6052789	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAFK	chr7:6052554-6052729	K562	blood:	n/a	chr7:6052595-6052610
18	MAFK	chr7:6052435-6052761	IMR90	lung:	n/a	chr7:6052595-6052610
19	POLR2A	chr7:6052525-6052821	K562	blood:	n/a	n/a
20	POLR2A	chr7:6052099-6052739	K562	blood:	n/a	n/a
21	FOXA1	chr7:6052452-6052722	T-47D	breast:	n/a	n/a
22	BRCA1	chr7:6052520-6052690	HepG2	liver:	n/a	n/a
23	MAFF	chr7:6052430-6052791	HepG2	liver:	n/a	chr7:6052593-6052611
24	FOXA1	chr7:6052353-6052843	HepG2	liver:	n/a	n/a
25	MAFK	chr7:6052508-6052741	Hela-S3	cervix:	n/a	chr7:6052595-6052610
26	MAFF	chr7:6052440-6052704	K562	blood:	n/a	chr7:6052593-6052611
27	POLR2A	chr7:6052144-6052571	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr7:6052078-6052814	Hela-S3	cervix:	n/a	n/a
29	ARID3A	chr7:6052455-6052645	HepG2	liver:	n/a	n/a
30	MAFK	chr7:6052432-6052815	HepG2	liver:	n/a	chr7:6052595-6052610
31	POLR2A	chr7:6051979-6052794	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6051523..6054079-chr7:6054548..6056374,3	MCF-7	breast:
2	chr7:6051732..6053681-chr7:6096916..6099067,2	MCF-7	breast:
3	chr7:6050222..6054296-chr7:6073659..6078644,4	K562	blood:
4	chr7:6051380..6054901-chr7:6142533..6145755,4	MCF-7	breast:
5	chr7:6048072..6051160-chr7:6051353..6054103,4	MCF-7	breast:
6	chr7:6046975..6049583-chr7:6051111..6054745,4	K562	blood:

Variant related genes	Relation type
PMS2	TF binding region
ENSG00000207217	TF binding region
ENSG00000106346	Chromatin interaction
ENSG00000122512	Chromatin interaction
ENSG00000106305	Chromatin interaction
ENSG00000252929	Chromatin interaction
ENSG00000086232	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

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[JPT][hapmap]
rs12702460	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702461	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702462	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702463	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12702464	0.88[ASN][1000 genomes]
rs12702468	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13240138	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13245536	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13311041	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1860462	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1986625	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2286680	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	0.88[ASN][1000 genomes]
rs3735295	0.95[TSI][hapmap]
rs3735296	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779107	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs525090	0.81[JPT][hapmap]
rs59901370	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6463525	0.90[ASN][1000 genomes]
rs6463527	0.81[JPT][hapmap]
rs6949598	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6953340	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6964944	0.83[EUR][1000 genomes]
rs6973250	0.85[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs6974270	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71524066	0.81[EUR][1000 genomes]
rs7781199	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7788051	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7799214	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7805798	0.92[EUR][1000 genomes];0.86[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	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
15	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
16	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
17	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
18	nsv1018388	chr7:6038713-6131169	Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2009115	PMS2	cis	cerebellum	SCAN
rs2009115	PMS2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6049200-6061800	Weak transcription	Fetal Brain Male	brain
2	chr7:6049400-6054600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr7:6049400-6054600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:6049400-6054800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr7:6049400-6054800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr7:6049400-6054800	Weak transcription	Gastric	stomach
7	chr7:6049400-6054800	Weak transcription	Spleen	Spleen
8	chr7:6049400-6055400	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr7:6049400-6055400	Weak transcription	Aorta	Aorta
10	chr7:6049400-6055800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr7:6049400-6055800	Weak transcription	Fetal Lung	lung
12	chr7:6049400-6056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:6049400-6056000	Weak transcription	Thymus	Thymus
14	chr7:6049400-6061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr7:6049600-6054800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:6049600-6060400	Weak transcription	Fetal Kidney	kidney
18	chr7:6049600-6060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr7:6049800-6053400	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr7:6049800-6054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:6049800-6054600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr7:6049800-6054800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:6049800-6055400	Weak transcription	Right Ventricle	heart
24	chr7:6050000-6052600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:6050000-6052800	Enhancers	Adipose Nuclei	Adipose
26	chr7:6050000-6054400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr7:6050000-6054600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr7:6050000-6054600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr7:6050000-6054600	Weak transcription	Primary T cells from cord blood	blood
30	chr7:6050000-6054600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr7:6050000-6054600	Weak transcription	HSMMtube	muscle
32	chr7:6050000-6055400	Weak transcription	Right Atrium	heart
33	chr7:6050000-6057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:6050000-6097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:6050200-6052800	Genic enhancers	K562	blood
36	chr7:6050200-6054600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:6050200-6054600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr7:6050200-6054600	Weak transcription	HUVEC	blood vessel
39	chr7:6050400-6053400	Strong transcription	HSMM	muscle
40	chr7:6050400-6053600	Enhancers	Duodenum Mucosa	Duodenum
41	chr7:6050400-6054200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr7:6050400-6065600	Strong transcription	Lung	lung
43	chr7:6050400-6065800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr7:6050400-6089400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr7:6050600-6052800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr7:6050600-6053000	Genic enhancers	HepG2	liver
49	chr7:6050600-6053400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr7:6050600-6053400	Enhancers	Placenta Amnion	Placenta Amnion

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