Variant report

Variant	rs4974623
Chromosome Location	chr4:1404415-1404416
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	HDAC2	chr4:1404273-1404507	H1-hESC	embryonic stem cell:	n/a	chr4:1404437-1404456
2	MAX	chr4:1404107-1404872	K562	blood:	n/a	chr4:1404733-1404742 chr4:1404733-1404742 chr4:1404732-1404743 chr4:1404732-1404743 chr4:1404680-1404687 chr4:1404732-1404743 chr4:1404734-1404741 chr4:1404733-1404743 chr4:1404507-1404517 chr4:1404732-1404742
3	SIN3AK20	chr4:1404134-1404757	MCF-7	breast:	n/a	n/a
4	HDAC2	chr4:1404222-1404596	HepG2	liver:	n/a	chr4:1404437-1404456
5	TAF7	chr4:1404257-1404548	K562	blood:	n/a	n/a
6	ZNF384	chr4:1404239-1404546	K562	blood:	n/a	n/a
7	MAX	chr4:1404124-1404707	MCF-7	breast:	n/a	chr4:1404680-1404687 chr4:1404507-1404517
8	MAZ	chr4:1404198-1404601	HepG2	liver:	n/a	chr4:1404507-1404517
9	MAX	chr4:1404182-1404566	K562	blood:	n/a	chr4:1404507-1404517
10	JUND	chr4:1404212-1404581	H1-hESC	embryonic stem cell:	n/a	n/a
11	MYC	chr4:1404240-1404534	K562	blood:	n/a	chr4:1404507-1404517
12	SIN3AK20	chr4:1404275-1404472	PFSK-1	brain:	n/a	n/a
13	USF2	chr4:1404252-1404663	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr4:1404167-1404638	SK-N-SH	brain:	n/a	chr4:1404507-1404517
15	MXI1	chr4:1404040-1404947	IMR90	lung:	n/a	n/a
16	REST	chr4:1403712-1405980	U87	brain:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404916-1404934 chr4:1404918-1404931 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404921-1404935 chr4:1405201-1405210 chr4:1404923-1404933 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404915-1404935 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
17	REST	chr4:1403749-1405137	MCF-7	breast:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404916-1404934 chr4:1404918-1404931 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404921-1404935 chr4:1404923-1404933 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404915-1404935 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
18	MXI1	chr4:1404165-1404629	H1-hESC	embryonic stem cell:	n/a	n/a
19	E2F6	chr4:1404251-1404468	K562	blood:	n/a	n/a
20	MAZ	chr4:1404196-1404603	K562	blood:	n/a	chr4:1404507-1404517
21	REST	chr4:1403750-1405071	MCF-7	breast:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404916-1404934 chr4:1404918-1404931 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404921-1404935 chr4:1404923-1404933 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404915-1404935 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
22	SIN3AK20	chr4:1404253-1404626	K562	blood:	n/a	n/a
23	CHD2	chr4:1404307-1404425	K562	blood:	n/a	chr4:1404401-1404411
24	REST	chr4:1404126-1404766	Hela-S3	cervix:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404442-1404451
25	POLR2A	chr4:1404243-1404573	HCT-116	colon:	n/a	n/a
26	EP300	chr4:1404138-1404572	ECC-1	luminal epithelium:	n/a	chr4:1404443-1404459
27	REST	chr4:1403857-1404955	A549	lung:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404916-1404934 chr4:1404918-1404931 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404921-1404935 chr4:1404923-1404933 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404915-1404935 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
28	POLR2A	chr4:1404220-1404432	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr4:1404205-1404596	HUVEC	blood vessel:	n/a	n/a
30	GATA3	chr4:1404194-1404567	T-47D	breast:	n/a	n/a
31	ZC3H11A	chr4:1404296-1404558	K562	blood:	n/a	n/a
32	ZBTB7A	chr4:1404214-1404602	K562	blood:	n/a	n/a
33	EP300	chr4:1404193-1404562	H1-hESC	embryonic stem cell:	n/a	chr4:1404443-1404459
34	FOXA1	chr4:1404238-1404464	T-47D	breast:	n/a	n/a
35	REST	chr4:1403626-1405444	PANC-1	pancreas:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404916-1404934 chr4:1404918-1404931 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404921-1404935 chr4:1405201-1405210 chr4:1404923-1404933 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404915-1404935 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
36	MAX	chr4:1404100-1404702	HepG2	liver:	n/a	chr4:1404680-1404687 chr4:1404507-1404517
37	SP4	chr4:1404261-1404556	H1-hESC	embryonic stem cell:	n/a	n/a
38	CBX3	chr4:1404217-1404525	K562	blood:	n/a	n/a
39	REST	chr4:1404088-1404801	SK-N-SH	brain:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
40	REST	chr4:1403797-1404835	HepG2	liver:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
41	MAX	chr4:1404100-1404626	A549	lung:	n/a	chr4:1404507-1404517
42	MAX	chr4:1404097-1404706	ECC-1	luminal epithelium:	n/a	chr4:1404680-1404687 chr4:1404507-1404517
43	CHD2	chr4:1404230-1404545	H1-hESC	embryonic stem cell:	n/a	chr4:1404401-1404411
44	POLR2A	chr4:1404292-1404483	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr4:1404292-1404533	IMR90	lung:	n/a	chr4:1404344-1404357
46	MYC	chr4:1404297-1404520	MCF-7	breast:	n/a	chr4:1404507-1404517
47	HDAC2	chr4:1404273-1404624	HepG2	liver:	n/a	chr4:1404437-1404456
48	REST	chr4:1403835-1404804	PANC-1	pancreas:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404088-1404106 chr4:1404442-1404451
49	TAF7	chr4:1404113-1404560	H1-hESC	embryonic stem cell:	n/a	n/a
50	REST	chr4:1404164-1404644	GM12878	blood:	n/a	chr4:1404436-1404456 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404447-1404456 chr4:1404443-1404456 chr4:1404436-1404450 chr4:1404437-1404455 chr4:1404438-1404448 chr4:1404440-1404453 chr4:1404436-1404456 chr4:1404442-1404451

No.	Distal block	Cell Line	Cell type
1	chr4:1339822..1342311-chr4:1403481..1406115,2	K562	blood:
2	chr4:1394639..1396218-chr4:1403445..1405898,2	MCF-7	breast:
3	chr4:1403430..1405914-chr4:1407635..1410239,2	K562	blood:
4	chr4:1398123..1401195-chr4:1402046..1405937,3	K562	blood:

Variant related genes	Relation type
NKX1-1	TF binding region
ENSG00000163945	Chromatin interaction
ENSG00000235608	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11248002	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11248004	0.85[ASN][1000 genomes]
rs12649865	0.95[ASN][1000 genomes]
rs4441710	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4974622	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7670672	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3339080	chr4:970630-1546223	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv878328	chr4:1141573-1990425	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv878330	chr4:1147407-1523930	Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv461152	chr4:1159680-1415698	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	nsv593278	chr4:1159680-1415698	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
7	nsv997971	chr4:1191256-1518521	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	67 gene(s)	inside rSNPs	diseases
8	nsv878344	chr4:1291337-1414684	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
9	nsv878345	chr4:1291337-1563920	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
10	nsv878347	chr4:1300077-1866358	Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
11	esv1794294	chr4:1307119-1817474	Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
12	nsv878350	chr4:1320023-1500753	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv878351	chr4:1329847-1414684	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
14	nsv1008785	chr4:1335089-1518521	Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv536988	chr4:1335089-1518521	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv593302	chr4:1338618-1414684	ZNF genes & repeats Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv870062	chr4:1376068-1523451	Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
18	nsv1003107	chr4:1380178-1710751	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv1005964	chr4:1380178-1949459	Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
20	nsv870084	chr4:1389629-1563818	ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
21	esv1821063	chr4:1391152-1420822	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
22	esv1829127	chr4:1391152-1496353	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	nsv878353	chr4:1392171-1549473	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
24	esv1799146	chr4:1392425-1423046	Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4974623	CRIPAK	Cis_1M	lymphoblastoid	RTeQTL
rs4974623	KIAA1530	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:1399800-1411200	Weak transcription	Right Atrium	heart
2	chr4:1402400-1405000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:1404400-1404600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr4:1404400-1404600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr4:1404400-1404600	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr4:1404400-1404600	Bivalent Enhancer	Fetal Stomach	stomach
7	chr4:1404400-1404600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
8	chr4:1404400-1404800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:1404400-1404800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr4:1404400-1404800	Bivalent Enhancer	Lung	lung
11	chr4:1404400-1404800	Enhancers	Ovary	ovary

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