Variant report

Variant	rs72850297
Chromosome Location	chr6:28220578-28220579
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	ZEB1	chr6:28220354-28220821	GM12878	blood:	n/a	n/a
2	POLR2A	chr6:28219726-28220805	HepG2	liver:	n/a	n/a
3	MYBL2	chr6:28219684-28220618	HepG2	liver:	n/a	n/a
4	POLR2A	chr6:28219413-28220765	GM19193	blood:	n/a	n/a
5	MAX	chr6:28219889-28220633	GM12878	blood:	n/a	chr6:28220361-28220371
6	TCF7L2	chr6:28219867-28220589	HCT-116	colon:	n/a	chr6:28220392-28220401 chr6:28220389-28220405 chr6:28220390-28220404 chr6:28220391-28220401 chr6:28220389-28220405
7	POLR2A	chr6:28219488-28220849	HL-60	blood:	n/a	n/a
8	POLR2A	chr6:28219358-28220731	GM19099	blood:	n/a	n/a
9	POLR2A	chr6:28219810-28220709	Raji	blood:	n/a	n/a
10	POLR2A	chr6:28219454-28220757	H1-neurons	neurons:	n/a	n/a
11	MTA3	chr6:28219429-28220978	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:28219452-28220836	GM12891	blood:	n/a	n/a
13	BHLHE40	chr6:28220562-28220595	K562	blood:	n/a	n/a
14	POLR2A	chr6:28220326-28220721	GM12878	blood:	n/a	n/a
15	BRCA1	chr6:28220499-28220591	HepG2	liver:	n/a	n/a
16	TEAD4	chr6:28219666-28221108	K562	blood:	n/a	chr6:28220592-28220601
17	REST	chr6:28219362-28220828	H1-neurons	neurons:	n/a	chr6:28220440-28220460 chr6:28220443-28220456
18	POLR2A	chr6:28219339-28220891	GM12878	blood:	n/a	n/a
19	HCFC1	chr6:28219508-28221194	Hela-S3	cervix:	n/a	n/a
20	SP2	chr6:28219678-28220742	HepG2	liver:	n/a	chr6:28220023-28220038
21	MAFF	chr6:28220523-28220698	HepG2	liver:	n/a	n/a
22	ZNF384	chr6:28220504-28220586	K562	blood:	n/a	n/a
23	CBX3	chr6:28219728-28220879	K562	blood:	n/a	n/a
24	POLR2A	chr6:28219391-28220860	GM18505	blood:	n/a	n/a
25	POLR2A	chr6:28219582-28220888	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:28220416-28220587	MCF-7	breast:	n/a	n/a
27	POLR2A	chr6:28220391-28220789	GM12891	blood:	n/a	n/a
28	POLR2A	chr6:28220569-28220705	GM12878	blood:	n/a	n/a
29	GABPA	chr6:28219221-28220691	MCF-7	breast:	n/a	n/a
30	MYC	chr6:28220578-28220587	MCF-7	breast:	n/a	n/a
31	JUN	chr6:28219429-28220813	K562	blood:	n/a	chr6:28220579-28220587
32	POLR2A	chr6:28219382-28220886	GM12891	blood:	n/a	n/a
33	ZNF263	chr6:28219534-28220641	HEK293-T-REx	kidney:	n/a	chr6:28220492-28220501
34	POLR2A	chr6:28220489-28220814	GM12891	blood:	n/a	n/a
35	POLR2A	chr6:28220432-28220639	Hela-S3	cervix:	n/a	n/a
36	TCF7L2	chr6:28219780-28220767	Hela-S3	cervix:	n/a	chr6:28220392-28220401 chr6:28220389-28220405 chr6:28220390-28220404 chr6:28220391-28220401 chr6:28220389-28220405
37	POLR2A	chr6:28219674-28220879	GM12878	blood:	n/a	n/a
38	TEAD4	chr6:28219861-28220772	K562	blood:	n/a	chr6:28220592-28220601
39	NRF1	chr6:28220361-28220656	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:28220340-28220785	GM12878	blood:	n/a	n/a
41	GABPA	chr6:28219433-28220610	A549	lung:	n/a	n/a
42	RELA	chr6:28219620-28220725	GM15510	blood:	n/a	n/a
43	POLR2A	chr6:28219750-28220872	HL-60	blood:	n/a	n/a
44	MXI1	chr6:28219483-28220848	SK-N-SH	brain:	n/a	n/a
45	POLR2A	chr6:28219248-28220771	K562	blood:	n/a	n/a
46	POLR2A	chr6:28219198-28220804	GM12892	blood:	n/a	n/a
47	RCOR1	chr6:28219862-28220579	HepG2	liver:	n/a	n/a
48	POLR2A	chr6:28219554-28220633	Hela-S3	cervix:	n/a	n/a
49	POLR2A	chr6:28219189-28220916	GM12892	blood:	n/a	n/a
50	POLR2A	chr6:28219429-28220805	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28220144..28224072-chr6:28306303..28309254,3	K562	blood:
2	chr6:28109464..28110985-chr6:28218502..28221254,2	MCF-7	breast:
3	chr6:28219780..28221874-chr6:28323231..28325438,2	K562	blood:
4	chr6:28192051..28194433-chr6:28219534..28221191,2	MCF-7	breast:
5	chr6:28105046..28106642-chr6:28218504..28220928,2	K562	blood:
6	chr6:28103203..28105926-chr6:28219159..28220709,2	MCF-7	breast:
7	chr6:28219546..28223731-chr6:28316147..28319107,5	K562	blood:
8	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
9	chr6:28217166..28222171-chr6:28233596..28237356,7	MCF-7	breast:
10	chr6:28219997..28223882-chr6:28224379..28228192,5	K562	blood:
11	chr6:28191711..28195552-chr6:28216768..28221883,5	MCF-7	breast:
12	chr6:28185564..28187470-chr6:28218621..28220714,2	MCF-7	breast:
13	chr6:28072503..28074418-chr6:28220133..28221944,2	K562	blood:
14	chr6:28218301..28221476-chr6:28302207..28305180,4	MCF-7	breast:
15	chr6:28103155..28106167-chr6:28220159..28222685,3	MCF-7	breast:
16	chr6:28220557..28222455-chr6:28320918..28322709,2	K562	blood:
17	chr6:28218514..28221776-chr6:28301462..28305432,7	K562	blood:
18	chr6:28218888..28222826-chr6:28224722..28227606,3	K562	blood:
19	chr6:28218194..28221046-chr6:28316270..28319035,4	K562	blood:

Variant related genes	Relation type
ZKSCAN4	TF binding region
ENSG00000235109	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000189134	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1150710	1.00[ASN][1000 genomes]
rs11546572	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2079705	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41269285	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41269287	1.00[ASN][1000 genomes]
rs41269289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269291	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41270579	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs41270589	1.00[AFR][1000 genomes]
rs4540253	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61744109	1.00[ASN][1000 genomes]
rs62620226	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72844204	1.00[AFR][1000 genomes]
rs72844212	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72844218	1.00[AFR][1000 genomes]
rs72844220	1.00[AFR][1000 genomes]
rs72846777	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846788	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846792	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72846797	1.00[ASN][1000 genomes]
rs72846802	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72848793	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849204	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849206	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849210	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849214	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72849222	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72850298	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72850299	1.00[AFR][1000 genomes]
rs72850300	1.00[AFR][1000 genomes]
rs72850302	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72851105	1.00[ASN][1000 genomes]
rs72851135	1.00[ASN][1000 genomes]
rs72851138	1.00[ASN][1000 genomes]
rs72851139	1.00[ASN][1000 genomes]
rs72851156	1.00[ASN][1000 genomes]
rs72851158	1.00[ASN][1000 genomes]
rs72851160	1.00[ASN][1000 genomes]
rs72851161	1.00[ASN][1000 genomes]
rs72851168	1.00[ASN][1000 genomes]
rs72851173	1.00[AFR][1000 genomes]
rs72851179	1.00[AFR][1000 genomes]
rs72851182	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854506	1.00[ASN][1000 genomes]
rs72854515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854521	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72854522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854524	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72854525	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854527	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854531	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854533	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72854535	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72854536	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs72854542	0.85[AMR][1000 genomes]
rs72854546	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72854553	0.85[AMR][1000 genomes]
rs72854556	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7752415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28218400-28220600	Active TSS	A549	lung
2	chr6:28218600-28220800	Flanking Active TSS	Liver	Liver
3	chr6:28219000-28220600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr6:28219000-28220600	Active TSS	Fetal Kidney	kidney
5	chr6:28219000-28220600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr6:28219000-28220800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr6:28219200-28220800	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr6:28219600-28220800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:28219800-28221000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr6:28220000-28220600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:28220000-28220600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:28220000-28220600	Flanking Active TSS	Stomach Mucosa	stomach
13	chr6:28220000-28220800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr6:28220000-28220800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr6:28220000-28220800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr6:28220000-28220800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr6:28220000-28220800	Flanking Active TSS	Brain Cingulate Gyrus	brain
18	chr6:28220000-28220800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr6:28220000-28220800	Flanking Active TSS	K562	blood
20	chr6:28220000-28221000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:28220200-28220600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
22	chr6:28220200-28220600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:28220200-28220600	Flanking Active TSS	H9 Cell Line	embryonic stem cell
24	chr6:28220200-28220600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:28220200-28220600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:28220200-28220600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr6:28220200-28220600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr6:28220200-28220600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr6:28220200-28220600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr6:28220200-28220600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
31	chr6:28220200-28220600	Flanking Active TSS	Primary B cells from peripheral blood	blood
32	chr6:28220200-28220600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
33	chr6:28220200-28220600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr6:28220200-28220600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr6:28220200-28220600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:28220200-28220600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr6:28220200-28220600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:28220200-28220600	Flanking Active TSS	Brain Germinal Matrix	brain
39	chr6:28220200-28220600	Flanking Active TSS	Colonic Mucosa	Colon
40	chr6:28220200-28220600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr6:28220200-28220600	Flanking Active TSS	Fetal Brain Male	brain
42	chr6:28220200-28220600	Flanking Active TSS	Fetal Brain Female	brain
43	chr6:28220200-28220600	Flanking Active TSS	Fetal Heart	heart
44	chr6:28220200-28220600	Flanking Active TSS	Fetal Intestine Large	intestine
45	chr6:28220200-28220600	Flanking Active TSS	Fetal Intestine Small	intestine
46	chr6:28220200-28220600	Flanking Active TSS	Fetal Muscle Trunk	muscle
47	chr6:28220200-28220600	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr6:28220200-28220600	Flanking Active TSS	Fetal Stomach	stomach
49	chr6:28220200-28220600	Flanking Active TSS	Fetal Thymus	thymus
50	chr6:28220200-28220600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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