Variant report

Variant	rs3779107
Chromosome Location	chr7:6055929-6055930
allele	C/T
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	EP300	chr7:6055247-6056137	ECC-1	luminal epithelium:	n/a	chr7:6055596-6055612
2	POLR2A	chr7:6055138-6056907	U87	brain:	n/a	n/a
3	CUX1	chr7:6055849-6056007	K562	blood:	n/a	n/a
4	ZNF143	chr7:6055587-6056091	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr7:6055840-6055990	AG09319	gingival:	n/a	n/a
6	ATF1	chr7:6055572-6055950	K562	blood:	n/a	n/a
7	NFIC	chr7:6055271-6056215	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr7:6055855-6056100	MCF-7	breast:	n/a	n/a
9	PML	chr7:6055355-6055939	K562	blood:	n/a	n/a
10	BCL3	chr7:6055646-6056158	A549	lung:	n/a	n/a
11	POLR2A	chr7:6055369-6057812	K562	blood:	n/a	n/a
12	JUND	chr7:6055566-6056528	K562	blood:	n/a	chr7:6056236-6056244 chr7:6056236-6056244 chr7:6056232-6056243 chr7:6056237-6056244
13	TBP	chr7:6055471-6056010	Hela-S3	cervix:	n/a	n/a
14	USF2	chr7:6055521-6056691	Hela-S3	cervix:	n/a	n/a
15	MAX	chr7:6055557-6056086	Hela-S3	cervix:	n/a	chr7:6055823-6055832
16	KAP1	chr7:6055560-6056352	HEK293	kidney:	n/a	chr7:6056237-6056246
17	STAT3	chr7:6055614-6055994	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr7:6055326-6055975	U87	brain:	n/a	n/a
19	ARID3A	chr7:6055533-6055954	K562	blood:	n/a	n/a
20	MAX	chr7:6055407-6056209	K562	blood:	n/a	chr7:6055823-6055832
21	GTF2F1	chr7:6055464-6056055	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr7:6055570-6056148	K562	blood:	n/a	chr7:6056060-6056072
23	POLR2A	chr7:6055299-6056951	H1-hESC	embryonic stem cell:	n/a	n/a
24	CEBPB	chr7:6055622-6055992	HepG2	liver:	n/a	n/a
25	POLR2A	chr7:6055436-6056864	A549	lung:	n/a	n/a
26	RFX5	chr7:6055564-6055952	Hela-S3	cervix:	n/a	n/a
27	TEAD4	chr7:6055346-6056270	ECC-1	luminal epithelium:	n/a	n/a
28	EP300	chr7:6055570-6056332	K562	blood:	n/a	chr7:6055596-6055612
29	MAZ	chr7:6055606-6055965	K562	blood:	n/a	chr7:6055823-6055832
30	CEBPB	chr7:6055589-6056080	IMR90	lung:	n/a	chr7:6056060-6056072
31	TCF7L2	chr7:6055504-6056153	PANC-1	pancreas:	n/a	n/a
32	RUNX3	chr7:6055736-6056135	GM12878	blood:	n/a	n/a
33	POLR2A	chr7:6055537-6056889	K562	blood:	n/a	n/a
34	BRCA1	chr7:6055576-6056081	Hela-S3	cervix:	n/a	n/a
35	MAFK	chr7:6055753-6055953	K562	blood:	n/a	n/a
36	E2F4	chr7:6055870-6056217	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr7:6055366-6056434	HCT-116	colon:	n/a	n/a
38	POLR2A	chr7:6055475-6056272	HepG2	liver:	n/a	n/a
39	POLR2A	chr7:6055700-6056739	GM12878	blood:	n/a	n/a
40	MYC	chr7:6055568-6056297	K562	blood:	n/a	chr7:6056235-6056244 chr7:6055823-6055832 chr7:6056272-6056282
41	POLR2A	chr7:6055494-6055971	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr7:6055306-6056303	PANC-1	pancreas:	n/a	n/a
43	CEBPB	chr7:6055508-6056064	ECC-1	luminal epithelium:	n/a	n/a
44	POLR2A	chr7:6055375-6057077	PANC-1	pancreas:	n/a	n/a
45	RCOR1	chr7:6055534-6055950	Hela-S3	cervix:	n/a	n/a
46	CEBPB	chr7:6055591-6056220	Hela-S3	cervix:	n/a	chr7:6056060-6056072
47	RAD21	chr7:6055562-6056074	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr7:6055388-6055934	GM12892	blood:	n/a	n/a
49	CEBPB	chr7:6055340-6056159	HCT-116	colon:	n/a	chr7:6056060-6056072
50	POLR2A	chr7:6055377-6056918	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:6055602..6058271-chr7:6142750..6144893,2	MCF-7	breast:
2	chr7:6054308..6057610-chr7:6144384..6145966,3	K562	blood:
3	chr7:6054346..6056159-chr7:6142852..6144380,2	K562	blood:
4	chr7:6055912..6057708-chr7:6097324..6099828,2	MCF-7	breast:
5	chr7:6046629..6049121-chr7:6054916..6059212,5	K562	blood:
6	chr7:6051523..6054079-chr7:6054548..6056374,3	MCF-7	breast:
7	chr7:6055317..6057272-chr7:6144133..6145966,2	K562	blood:

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

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

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	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702461	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702462	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702463	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12702464	0.90[ASN][1000 genomes]
rs12702468	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240138	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13245536	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13311041	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1860462	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1986625	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2009115	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]
rs2286680	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]
rs2302332	0.81[JPT][hapmap]
rs34197105	0.90[ASN][1000 genomes]
rs3735295	0.95[TSI][hapmap]
rs3735296	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3779109	0.85[CEU][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes]
rs525090	0.81[JPT][hapmap]
rs59901370	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6463525	0.93[ASN][1000 genomes]
rs6463527	0.81[JPT][hapmap]
rs6949598	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6953340	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6973250	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs6974270	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6979676	0.86[MKK][hapmap]
rs7781199	0.87[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7788051	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7799214	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7805798	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3779107	KIAA0415	cis	cerebellum	SCAN
rs3779107	PMS2	cis	cerebellum	SCAN
rs3779107	PMS2	cis	parietal	SCAN

Chromatin state (count:127 , 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	chr7:6049400-6056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr7:6049400-6056000	Weak transcription	Thymus	Thymus
4	chr7:6049400-6061400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr7:6049400-6098000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:6049600-6060400	Weak transcription	Fetal Kidney	kidney
7	chr7:6049600-6060600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:6050000-6057200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr7:6050000-6097800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr7:6050400-6065600	Strong transcription	Lung	lung
11	chr7:6050400-6065800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr7:6050400-6089400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr7:6050400-6095400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:6050400-6095600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:6050600-6057600	Strong transcription	Primary hematopoietic stem cells	blood
16	chr7:6050600-6070000	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr7:6050600-6091000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:6050800-6062000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:6050800-6091000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr7:6050800-6095200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr7:6051000-6062200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr7:6051000-6095200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr7:6051800-6089600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:6052200-6089400	Strong transcription	Fetal Stomach	stomach
25	chr7:6052400-6062000	Weak transcription	Small Intestine	intestine
26	chr7:6052600-6094600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr7:6053000-6095000	Strong transcription	Fetal Intestine Small	intestine
28	chr7:6054000-6066000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr7:6054200-6065800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr7:6054200-6076200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr7:6054400-6063600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr7:6054400-6068600	Strong transcription	Fetal Brain Female	brain
33	chr7:6054400-6070200	Strong transcription	H9 Cell Line	embryonic stem cell
34	chr7:6054400-6095200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr7:6054600-6056000	Enhancers	HSMMtube	muscle
36	chr7:6054600-6056200	Genic enhancers	NHEK	skin
37	chr7:6054600-6056400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:6054600-6056400	Genic enhancers	Dnd41	blood
39	chr7:6054600-6056400	Genic enhancers	K562	blood
40	chr7:6054600-6056600	Genic enhancers	Brain Inferior Temporal Lobe	brain
41	chr7:6054600-6056600	Genic enhancers	Fetal Muscle Leg	muscle
42	chr7:6054600-6056800	Genic enhancers	Muscle Satellite Cultured Cells	--
43	chr7:6054600-6057200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
44	chr7:6054600-6057800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:6054600-6058000	Strong transcription	Brain Germinal Matrix	brain
46	chr7:6054600-6059200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:6054600-6059400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:6054600-6063000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr7:6054600-6063600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr7:6054600-6063600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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