Variant report

Variant	rs41296680
Chromosome Location	chr1:213030982-213030983
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	CREB1	chr1:213030786-213032031	GM12878	blood:	n/a	n/a
2	ZBTB7A	chr1:213030931-213032339	K562	blood:	n/a	n/a
3	GATA2	chr1:213030826-213031237	K562	blood:	n/a	n/a
4	SIN3AK20	chr1:213030942-213032476	PANC-1	pancreas:	n/a	n/a
5	GATA3	chr1:213030775-213031342	MCF-7	breast:	n/a	n/a
6	TAF1	chr1:213030944-213031874	H1-hESC	embryonic stem cell:	n/a	n/a
7	HDAC2	chr1:213030916-213031817	HepG2	liver:	n/a	n/a
8	ZNF384	chr1:213030549-213031823	K562	blood:	n/a	n/a
9	TAF1	chr1:213030865-213031797	K562	blood:	n/a	n/a
10	POLR2A	chr1:213030857-213032406	GM18505	blood:	n/a	n/a
11	UBTF	chr1:213030900-213032562	K562	blood:	n/a	n/a
12	MAX	chr1:213030940-213032497	SK-N-SH	brain:	n/a	chr1:213031632-213031639
13	HCFC1	chr1:213030774-213032525	Hela-S3	cervix:	n/a	n/a
14	USF2	chr1:213030948-213031422	Hela-S3	cervix:	n/a	n/a
15	MXI1	chr1:213030966-213032442	HepG2	liver:	n/a	n/a
16	ZNF263	chr1:213030951-213032903	HEK293-T-REx	kidney:	n/a	chr1:213031610-213031619
17	POLR2A	chr1:213029909-213032745	GM12891	blood:	n/a	n/a
18	CREB1	chr1:213030803-213031879	A549	lung:	n/a	n/a
19	POLR2A	chr1:213030952-213032496	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:213030920-213031918	GM12892	blood:	n/a	n/a
21	TEAD4	chr1:213030852-213031670	HepG2	liver:	n/a	n/a
22	GATA3	chr1:213030830-213032386	A549	lung:	n/a	n/a
23	POLR2A	chr1:213030858-213032515	GM12892	blood:	n/a	n/a
24	POLR2A	chr1:213030919-213032607	HL-60	blood:	n/a	n/a
25	RCOR1	chr1:213030771-213032596	K562	blood:	n/a	n/a
26	POLR2A	chr1:213030923-213031899	PANC-1	pancreas:	n/a	n/a
27	MAX	chr1:213030929-213032442	ECC-1	luminal epithelium:	n/a	chr1:213031632-213031639
28	TEAD4	chr1:213030903-213031864	ECC-1	luminal epithelium:	n/a	n/a
29	KAP1	chr1:213030968-213031579	U2OS	brain:	n/a	n/a
30	HDAC2	chr1:213030916-213031800	K562	blood:	n/a	n/a
31	TAL1	chr1:213030917-213031878	K562	blood:	n/a	n/a
32	POLR2A	chr1:213030910-213031979	Hela-S3	cervix:	n/a	n/a
33	SIN3AK20	chr1:213030981-213032041	MCF-7	breast:	n/a	n/a
34	CREB1	chr1:213030908-213031908	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:213030869-213032593	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:213030873-213032575	H1-hESC	embryonic stem cell:	n/a	n/a
37	ZBTB33	chr1:213030974-213031805	A549	lung:	n/a	chr1:213031501-213031511
38	POLR2A	chr1:213030914-213032666	HepG2	liver:	n/a	n/a
39	ATF1	chr1:213030963-213031732	K562	blood:	n/a	n/a
40	JUN	chr1:213030959-213031685	K562	blood:	n/a	chr1:213031526-213031535 chr1:213031462-213031471
41	TAF1	chr1:213030971-213031851	A549	lung:	n/a	n/a
42	EP300	chr1:213030920-213031255	SK-N-SH_RA	brain:	n/a	n/a
43	POLR2A	chr1:213030941-213031107	A549	lung:	n/a	n/a
44	POLR2A	chr1:213030954-213031881	K562	blood:	n/a	n/a
45	MAFK	chr1:213030940-213031288	IMR90	lung:	n/a	chr1:213031116-213031131
46	PML	chr1:213030792-213032476	GM12878	blood:	n/a	n/a
47	POLR2A	chr1:213030948-213031794	GM12878	blood:	n/a	n/a
48	MAX	chr1:213030930-213031994	H1-hESC	embryonic stem cell:	n/a	chr1:213031632-213031639
49	TEAD4	chr1:213030853-213031860	K562	blood:	n/a	n/a
50	SP1	chr1:213030880-213031873	A549	lung:	n/a	chr1:213031571-213031580 chr1:213031460-213031474 chr1:213031517-213031538 chr1:213031569-213031581 chr1:213031757-213031766 chr1:213031569-213031581 chr1:213031565-213031578 chr1:213031756-213031765 chr1:213031695-213031709 chr1:213031461-213031470 chr1:213031459-213031470

No.	Distal block	Cell Line	Cell type
1	chr1:213026064..213028809-chr1:213029690..213032627,2	K562	blood:
2	chr1:213025871..213028763-chr1:213030169..213033277,3	MCF-7	breast:
3	chr1:213025489..213028696-chr1:213029248..213033184,3	K562	blood:
4	chr1:212779176..212786217-chr1:213030148..213034937,8	K562	blood:
5	chr1:212977806..212980707-chr1:213030715..213033244,2	K562	blood:
6	chr1:213030101..213032938-chr1:213186047..213190102,3	K562	blood:
7	chr1:213019184..213021421-chr1:213029036..213031526,2	K562	blood:
8	chr1:212965176..212966735-chr1:213030010..213031816,2	K562	blood:
9	chr1:212963280..212966676-chr1:213030010..213031803,4	K562	blood:

Variant related genes	Relation type
FLVCR1	TF binding region
ENSG00000236317	TF binding region
ENSG00000174606	Chromatin interaction
ENSG00000185523	Chromatin interaction
ENSG00000235182	Chromatin interaction
ENSG00000203705	Chromatin interaction
ENSG00000117697	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000236317	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2047288	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047291	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088256	1.00[AFR][1000 genomes]
rs3738799	1.00[AMR][1000 genomes]
rs3738801	1.00[AMR][1000 genomes]
rs3768549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41258005	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41275386	1.00[AMR][1000 genomes]
rs41296666	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296668	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296674	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296676	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41297452	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300027	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300033	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300035	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300043	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41300979	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41301029	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs41307644	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41307646	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41314540	1.00[AMR][1000 genomes]
rs41314542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56300028	0.85[AMR][1000 genomes]
rs58746017	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73079880	0.85[AMR][1000 genomes]
rs73079886	0.85[AMR][1000 genomes]
rs73079887	0.85[AMR][1000 genomes]
rs7521050	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001637	chr1:212907611-213034606	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1011186	chr1:213005165-213069563	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1013705	chr1:213005344-213064209	Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv1008383	chr1:213025546-213114894	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv998261	chr1:213029814-213064209	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv998979	chr1:213029814-213073013	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:213029600-213033200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:213029600-213033400	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr1:213029800-213032000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr1:213030000-213031000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:213030000-213031200	Flanking Active TSS	Dnd41	blood
6	chr1:213030000-213032800	Active TSS	Rectal Smooth Muscle	rectum
7	chr1:213030200-213031000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:213030200-213031000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:213030200-213031000	Flanking Active TSS	Colon Smooth Muscle	Colon
10	chr1:213030200-213031000	Enhancers	Stomach Mucosa	stomach
11	chr1:213030200-213031200	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr1:213030400-213031000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr1:213030400-213031000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:213030400-213031000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr1:213030400-213031000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:213030400-213031000	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr1:213030400-213031200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr1:213030400-213031200	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr1:213030400-213031200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr1:213030400-213031200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:213030400-213031200	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr1:213030400-213031200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
23	chr1:213030400-213031200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr1:213030400-213031200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:213030400-213031200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr1:213030400-213031400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr1:213030400-213031800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:213030400-213032200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:213030400-213032200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr1:213030400-213033400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:213030400-213034000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:213030400-213034000	Active TSS	HSMM	muscle
33	chr1:213030400-213034600	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr1:213030400-213035600	Active TSS	H9 Cell Line	embryonic stem cell
35	chr1:213030600-213031000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:213030600-213031000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr1:213030600-213031000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr1:213030600-213031000	Active TSS	HepG2	liver
39	chr1:213030600-213031000	Flanking Active TSS	NH-A	brain
40	chr1:213030600-213031200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
41	chr1:213030600-213031200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
42	chr1:213030600-213031200	Flanking Active TSS	Primary hematopoietic stem cells	blood
43	chr1:213030600-213031200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
44	chr1:213030600-213031200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr1:213030600-213031200	Flanking Active TSS	Fetal Muscle Trunk	muscle
46	chr1:213030600-213031200	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr1:213030600-213031200	Flanking Active TSS	Placenta	Placenta
48	chr1:213030600-213031200	Flanking Active TSS	HUVEC	blood vessel
49	chr1:213030600-213031400	Flanking Active TSS	Fetal Thymus	thymus
50	chr1:213030600-213031400	Active TSS	Right Atrium	heart

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