Variant report

Variant	rs28391170
Chromosome Location	chr4:106629246-106629247
allele	A/C
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	SIN3AK20	chr4:106629223-106630399	HCT-116	colon:	n/a	n/a
2	MYC	chr4:106628951-106630488	NB4	blood:	n/a	n/a
3	POLR2A	chr4:106629046-106630707	HL-60	blood:	n/a	n/a
4	SIN3AK20	chr4:106629195-106630579	MCF-7	breast:	n/a	n/a
5	E2F6	chr4:106629083-106630441	K562	blood:	n/a	chr4:106630312-106630324
6	TBP	chr4:106629185-106630644	Hela-S3	cervix:	n/a	n/a
7	TBP	chr4:106629046-106630581	K562	blood:	n/a	n/a
8	RELA	chr4:106629193-106630118	GM19099	blood:	n/a	n/a
9	POLR2A	chr4:106629226-106630450	PFSK-1	brain:	n/a	n/a
10	JUND	chr4:106629121-106630414	K562	blood:	n/a	n/a
11	MXI1	chr4:106628998-106630475	GM12878	blood:	n/a	n/a
12	JUN	chr4:106628881-106630697	K562	blood:	n/a	n/a
13	POLR2A	chr4:106629154-106630804	H1-hESC	embryonic stem cell:	n/a	n/a
14	WRNIP1	chr4:106629169-106630251	GM12878	blood:	n/a	n/a
15	ARID3A	chr4:106628952-106629378	HepG2	liver:	n/a	n/a
16	STAT5A	chr4:106629160-106630210	GM12878	blood:	n/a	chr4:106629532-106629540
17	SREBP1	chr4:106628160-106630350	GM12878	blood:	n/a	n/a
18	MAX	chr4:106628916-106630623	K562	blood:	n/a	n/a
19	MAX	chr4:106629075-106630356	K562	blood:	n/a	n/a
20	TCF7L2	chr4:106629238-106630279	HCT-116	colon:	n/a	chr4:106629405-106629414 chr4:106629407-106629423 chr4:106629407-106629423 chr4:106629402-106629418 chr4:106629402-106629418
21	POLR2A	chr4:106629072-106630710	SK-N-MC	brain:	n/a	n/a
22	POLR2A	chr4:106629107-106630746	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:106628643-106630648	HepG2	liver:	n/a	n/a
24	POLR2A	chr4:106629032-106630622	Raji	blood:	n/a	n/a
25	MAX	chr4:106628974-106630154	NB4	blood:	n/a	n/a
26	MAX	chr4:106628902-106630416	HepG2	liver:	n/a	n/a
27	BHLHE40	chr4:106628688-106630088	K562	blood:	n/a	n/a
28	POLR2A	chr4:106629131-106630636	K562	blood:	n/a	n/a
29	POLR2A	chr4:106628823-106630756	K562	blood:	n/a	n/a
30	MYC	chr4:106628969-106630574	K562	blood:	n/a	n/a
31	MYC	chr4:106628960-106630149	MCF10A-Er-Src	breast:	n/a	n/a
32	CREB1	chr4:106629217-106630290	GM12878	blood:	n/a	n/a
33	MXI1	chr4:106628559-106631071	SK-N-SH	brain:	n/a	n/a
34	REST	chr4:106628973-106630806	H1-neurons	neurons:	n/a	n/a
35	MAX	chr4:106629093-106630661	Hela-S3	cervix:	n/a	n/a
36	SIN3AK20	chr4:106629187-106630039	H1-hESC	embryonic stem cell:	n/a	n/a
37	GABPA	chr4:106629209-106630471	A549	lung:	n/a	chr4:106629588-106629597
38	GABPA	chr4:106629147-106630778	MCF-7	breast:	n/a	chr4:106629588-106629597
39	MAZ	chr4:106629181-106630182	GM12878	blood:	n/a	n/a
40	POLR2A	chr4:106629033-106630612	PBDE	blood:	n/a	n/a
41	RAD21	chr4:106629074-106630113	IMR90	lung:	n/a	n/a
42	MXI1	chr4:106629177-106630602	HepG2	liver:	n/a	n/a
43	MYC	chr4:106629012-106630200	K562	blood:	n/a	n/a
44	PML	chr4:106628996-106630344	GM12878	blood:	n/a	n/a
45	BHLHE40	chr4:106628947-106630474	HepG2	liver:	n/a	n/a
46	RFX5	chr4:106628987-106632419	SK-N-SH	brain:	n/a	chr4:106629352-106629361 chr4:106630732-106630749 chr4:106631958-106631972 chr4:106631963-106631971 chr4:106631960-106631969 chr4:106631957-106631972
47	MAZ	chr4:106629064-106630781	IMR90	lung:	n/a	n/a
48	POLR2A	chr4:106629140-106630663	K562	blood:	n/a	n/a
49	HCFC1	chr4:106629151-106630387	Hela-S3	cervix:	n/a	n/a
50	POLR2A	chr4:106628754-106631181	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:106600442..106602529-chr4:106626797..106629772,2	K562	blood:
2	chr4:106628392..106631014-chr4:106816298..106818181,3	MCF-7	breast:
3	chr4:106628549..106631300-chr4:106636039..106639035,3	MCF-7	breast:
4	chr4:106393199..106396342-chr4:106628328..106631625,4	K562	blood:
5	chr4:106619847..106624541-chr4:106627186..106631133,7	MCF-7	breast:
6	chr4:106393678..106396634-chr4:106628055..106631625,3	K562	blood:
7	chr4:106616699..106623307-chr4:106623731..106631342,11	K562	blood:
8	chr4:106628554..106633489-chr4:106634205..106639726,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGEF38-1	chr4:106629058-106629250	ENSG00000249823.1

Variant related genes	Relation type
GSTCD	TF binding region
INTS12	TF binding region
ENSG00000138785	Chromatin interaction
ENSG00000138780	Chromatin interaction
ENSG00000248778	Chromatin interaction
ENSG00000168743	Chromatin interaction
ENSG00000236699	Chromatin interaction
ENSG00000138777	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10019217	0.85[ASN][1000 genomes]
rs10030620	0.80[ASN][1000 genomes]
rs10049527	0.82[ASN][1000 genomes]
rs10516522	1.00[ASN][1000 genomes]
rs11930244	0.87[ASN][1000 genomes]
rs11930965	0.90[ASN][1000 genomes]
rs11936611	0.82[ASN][1000 genomes]
rs12504088	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12511885	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512339	0.90[ASN][1000 genomes]
rs13110070	0.85[ASN][1000 genomes]
rs13145251	0.83[ASN][1000 genomes]
rs17036093	0.97[ASN][1000 genomes]
rs17036097	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17036102	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036158	0.92[ASN][1000 genomes]
rs17036254	0.82[ASN][1000 genomes]
rs2193852	0.92[ASN][1000 genomes]
rs2193853	0.92[ASN][1000 genomes]
rs28370551	1.00[ASN][1000 genomes]
rs28450989	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28559909	0.97[ASN][1000 genomes]
rs28698939	0.85[ASN][1000 genomes]
rs3796926	1.00[ASN][1000 genomes]
rs4235415	0.87[ASN][1000 genomes]
rs4490460	1.00[ASN][1000 genomes]
rs4698950	0.93[ASN][1000 genomes]
rs4698951	0.92[ASN][1000 genomes]
rs4699192	0.85[ASN][1000 genomes]
rs4699193	1.00[ASN][1000 genomes]
rs4699194	1.00[ASN][1000 genomes]
rs4699195	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4699197	1.00[ASN][1000 genomes]
rs4699198	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4699199	0.92[ASN][1000 genomes]
rs58388061	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58914657	0.83[ASN][1000 genomes]
rs59961848	0.84[ASN][1000 genomes]
rs60774107	0.97[ASN][1000 genomes]
rs60861135	0.92[ASN][1000 genomes]
rs6817029	0.88[ASN][1000 genomes]
rs6820671	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6825379	0.82[ASN][1000 genomes]
rs6826631	0.82[ASN][1000 genomes]
rs6843771	0.82[ASN][1000 genomes]
rs7658055	0.82[ASN][1000 genomes]
rs7659526	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7665588	0.92[ASN][1000 genomes]
rs7696836	0.85[ASN][1000 genomes]
rs7697619	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106627800-106630800	Active TSS	GM12878-XiMat	blood
2	chr4:106628000-106629800	Active TSS	Right Atrium	heart
3	chr4:106628200-106629400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:106628400-106629400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
5	chr4:106628400-106629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:106628400-106631000	Active TSS	Psoas Muscle	Psoas
7	chr4:106628600-106629400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
8	chr4:106628600-106629400	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr4:106628600-106629400	Flanking Active TSS	Brain Substantia Nigra	brain
10	chr4:106628600-106629400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr4:106628600-106629600	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr4:106628600-106629600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:106628600-106629600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr4:106628600-106630400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr4:106628600-106630400	Active TSS	Stomach Smooth Muscle	stomach
16	chr4:106628600-106630800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr4:106628600-106630800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr4:106628600-106630800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr4:106628600-106630800	Active TSS	Aorta	Aorta
20	chr4:106628600-106630800	Active TSS	Ovary	ovary
21	chr4:106628600-106631000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr4:106628600-106631800	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr4:106628800-106629400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr4:106628800-106629400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:106628800-106629400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr4:106628800-106629600	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr4:106628800-106629600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr4:106628800-106629600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr4:106628800-106629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:106628800-106629600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr4:106628800-106630200	Active TSS	Primary T cells fromperipheralblood	blood
32	chr4:106628800-106630200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:106628800-106630400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr4:106628800-106630400	Active TSS	Colonic Mucosa	Colon
35	chr4:106628800-106630800	Active TSS	Fetal Muscle Trunk	muscle
36	chr4:106628800-106630800	Active TSS	Left Ventricle	heart
37	chr4:106628800-106631000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr4:106628800-106631000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:106628800-106631000	Active TSS	Fetal Intestine Large	intestine
40	chr4:106628800-106631000	Active TSS	Fetal Muscle Leg	muscle
41	chr4:106628800-106631000	Active TSS	Fetal Thymus	thymus
42	chr4:106628800-106631000	Active TSS	Right Ventricle	heart
43	chr4:106628800-106631400	Active TSS	H1 Cell Line	embryonic stem cell
44	chr4:106628800-106631400	Active TSS	A549	lung
45	chr4:106628800-106631600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:106628800-106631800	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr4:106628800-106631800	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr4:106629000-106629400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
49	chr4:106629000-106629400	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr4:106629000-106629400	Active TSS	Primary T helper naive cells fromperipheralblood	blood

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