Variant report

Variant	rs10942702
Chromosome Location	chr5:70882535-70882536
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	MYC	chr5:70882130-70883653	K562	blood:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
2	MYBL2	chr5:70881842-70883381	HepG2	liver:	n/a	n/a
3	MAX	chr5:70881980-70883895	HepG2	liver:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
4	POLR2A	chr5:70882522-70883509	GM12878	blood:	n/a	n/a
5	POLR2A	chr5:70882198-70883597	GM12878	blood:	n/a	n/a
6	POLR2A	chr5:70882433-70883823	GM12891	blood:	n/a	n/a
7	MTA3	chr5:70882525-70883641	GM12878	blood:	n/a	n/a
8	RELA	chr5:70882338-70883846	GM15510	blood:	n/a	n/a
9	TBP	chr5:70882191-70883777	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:70882416-70883830	Hela-S3	cervix:	n/a	n/a
11	BHLHE40	chr5:70882158-70883641	K562	blood:	n/a	chr5:70883491-70883512
12	POU2F2	chr5:70882462-70883376	GM12891	blood:	n/a	n/a
13	MYC	chr5:70882130-70883321	K562	blood:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
14	TAF1	chr5:70882318-70883393	K562	blood:	n/a	n/a
15	HCFC1	chr5:70882080-70883740	Hela-S3	cervix:	n/a	n/a
16	TAF1	chr5:70882532-70883504	HepG2	liver:	n/a	n/a
17	HEY1	chr5:70882118-70883859	K562	blood:	n/a	chr5:70883102-70883111
18	HEY1	chr5:70882180-70883365	K562	blood:	n/a	chr5:70883102-70883111
19	IRF1	chr5:70881660-70883313	K562	blood:	n/a	chr5:70883045-70883054 chr5:70883059-70883073 chr5:70882354-70882375 chr5:70882377-70882398
20	ATF2	chr5:70882534-70883150	GM12878	blood:	n/a	n/a
21	ZBTB7A	chr5:70882491-70883279	K562	blood:	n/a	n/a
22	POLR2A	chr5:70882120-70883466	PANC-1	pancreas:	n/a	n/a
23	MAX	chr5:70882073-70883731	HepG2	liver:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
24	RFX5	chr5:70882350-70883329	K562	blood:	n/a	n/a
25	PML	chr5:70882433-70883450	K562	blood:	n/a	chr5:70883130-70883138
26	MAX	chr5:70882491-70883479	HUVEC	blood vessel:	n/a	chr5:70883100-70883110
27	MYC	chr5:70882084-70883802	K562	blood:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70883100-70883110 chr5:70882221-70882232
28	POLR2A	chr5:70882141-70883315	HepG2	liver:	n/a	n/a
29	E2F6	chr5:70882079-70883762	K562	blood:	n/a	chr5:70883243-70883252 chr5:70883089-70883098
30	TAF1	chr5:70882279-70883869	H1-hESC	embryonic stem cell:	n/a	n/a
31	TCF12	chr5:70882395-70883557	A549	lung:	n/a	chr5:70882906-70882915
32	POLR2A	chr5:70882331-70883800	GM15510	blood:	n/a	n/a
33	SIN3AK20	chr5:70882492-70883600	SK-N-SH	brain:	n/a	n/a
34	HCFC1	chr5:70882130-70883794	K562	blood:	n/a	n/a
35	POLR2A	chr5:70882231-70883811	GM19099	blood:	n/a	n/a
36	SIN3A	chr5:70882515-70883869	GM12878	blood:	n/a	n/a
37	POLR2A	chr5:70882196-70883799	HepG2	liver:	n/a	n/a
38	MAX	chr5:70882071-70882539	K562	blood:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70882221-70882232
39	CBX3	chr5:70882034-70883396	K562	blood:	n/a	n/a
40	ATF2	chr5:70882465-70883448	GM12878	blood:	n/a	n/a
41	CHD2	chr5:70882477-70883881	H1-hESC	embryonic stem cell:	n/a	n/a
42	SP1	chr5:70882215-70883314	HepG2	liver:	n/a	chr5:70883060-70883070 chr5:70883059-70883071 chr5:70883060-70883070 chr5:70883059-70883071
43	POU2F2	chr5:70882124-70883493	GM12878	blood:	n/a	n/a
44	MAX	chr5:70882018-70882578	MCF-7	breast:	n/a	chr5:70882224-70882231 chr5:70882222-70882231 chr5:70882221-70882232 chr5:70882220-70882233 chr5:70882221-70882232
45	POLR2A	chr5:70882470-70883703	PBDE	blood:	n/a	n/a
46	POLR2A	chr5:70882398-70883866	GM12891	blood:	n/a	n/a
47	POLR2A	chr5:70882155-70883533	HepG2	liver:	n/a	n/a
48	POLR2A	chr5:70881697-70884039	HepG2	liver:	n/a	n/a
49	MXI1	chr5:70881905-70883803	HepG2	liver:	n/a	n/a
50	POLR2A	chr5:70882426-70883844	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:70882161..70884487-chr5:70891024..70893721,4	MCF-7	breast:
2	chr5:70749978..70751854-chr5:70881938..70884932,2	K562	blood:
3	chr5:70881577..70886916-chr5:70891929..70900227,16	MCF-7	breast:
4	chr5:70880665..70885311-chr5:70885640..70890340,6	K562	blood:
5	chr5:70880133..70886735-chr5:70895650..70901637,10	MCF-7	breast:
6	chr5:70881870..70884694-chr5:70885301..70891902,7	MCF-7	breast:
7	chr17:58754114..58755898-chr5:70882002..70883719,2	MCF-7	breast:

Variant related genes	Relation type
MCCC2	TF binding region
ENSG00000145734	Chromatin interaction
ENSG00000141376	Chromatin interaction
ENSG00000131844	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10044572	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055460	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10060578	0.85[EUR][1000 genomes]
rs10064079	0.80[TSI][hapmap]
rs10064099	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10077085	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10434642	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10474383	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10805884	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10942284	0.85[EUR][1000 genomes]
rs10942533	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10942682	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10942700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10942705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743135	0.89[EUR][1000 genomes]
rs11746722	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152748	0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12153571	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12514732	0.89[EUR][1000 genomes]
rs12516456	1.00[CEU][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs12652715	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13157835	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748043	0.89[EUR][1000 genomes]
rs4062889	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4505929	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5005863	0.82[EUR][1000 genomes]
rs62361818	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs6452722	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6452900	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6453013	0.83[EUR][1000 genomes]
rs6453014	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6453018	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6453035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453043	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6872235	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6872671	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6877289	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6877773	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6886336	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6898471	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs715747	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7378662	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7380115	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7380280	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7444322	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7447726	0.85[EUR][1000 genomes]
rs7448422	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7449316	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7714527	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7715648	0.85[EUR][1000 genomes]
rs7721179	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7727576	0.85[EUR][1000 genomes]
rs7728577	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7735544	0.83[EUR][1000 genomes]
rs9968768	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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	nsv1034703	chr5:70391173-70995695	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv2754424	chr5:70749744-70885544	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv830340	chr5:70797113-70967110	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10942702	MCCC2	Cis_1M	lymphoblastoid	RTeQTL
rs10942702	CENPH	cis	parietal	SCAN
rs10942702	FAM169A	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:70864600-70882600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:70870400-70882600	Weak transcription	Fetal Heart	heart
3	chr5:70881800-70883600	Active TSS	Breast Myoepithelial Primary Cells	Breast
4	chr5:70881800-70884200	Active TSS	K562	blood
5	chr5:70882000-70884000	Active TSS	Ovary	ovary
6	chr5:70882000-70884200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr5:70882000-70884200	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:70882000-70884600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:70882200-70882600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr5:70882200-70882600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:70882200-70882600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr5:70882200-70882600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:70882200-70882600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:70882200-70882600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:70882200-70882600	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr5:70882200-70882600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr5:70882200-70882600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:70882200-70882600	Flanking Active TSS	Duodenum Mucosa	Duodenum
19	chr5:70882200-70882600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr5:70882200-70882600	Enhancers	Pancreas	Pancrea
21	chr5:70882200-70882600	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr5:70882200-70882600	Flanking Active TSS	Stomach Smooth Muscle	stomach
23	chr5:70882200-70882600	Enhancers	Spleen	Spleen
24	chr5:70882200-70882600	Enhancers	NHDF-Ad	bronchial
25	chr5:70882200-70882800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
26	chr5:70882200-70882800	Flanking Active TSS	Primary B cells from peripheral blood	blood
27	chr5:70882200-70882800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr5:70882200-70882800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr5:70882200-70882800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
30	chr5:70882200-70882800	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr5:70882200-70882800	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr5:70882200-70882800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr5:70882200-70882800	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr5:70882200-70882800	Flanking Active TSS	Placenta	Placenta
35	chr5:70882200-70882800	Flanking Active TSS	Osteobl	bone
36	chr5:70882200-70883000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr5:70882200-70883000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
38	chr5:70882200-70883000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
39	chr5:70882200-70883000	Flanking Active TSS	Liver	Liver
40	chr5:70882200-70883000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr5:70882200-70883000	Flanking Active TSS	Dnd41	blood
42	chr5:70882200-70883000	Flanking Active TSS	Hela-S3	cervix
43	chr5:70882200-70883400	Active TSS	Brain Substantia Nigra	brain
44	chr5:70882200-70883400	Active TSS	NHLF	lung
45	chr5:70882200-70883600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:70882200-70883600	Active TSS	Brain Hippocampus Middle	brain
47	chr5:70882200-70883600	Active TSS	Fetal Muscle Trunk	muscle
48	chr5:70882200-70883800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr5:70882200-70883800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:70882200-70883800	Bivalent/Poised TSS	HepG2	liver

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