Variant report

Variant	rs6705628
Chromosome Location	chr2:74208362-74208363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:175)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:175 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:74208250-74208790	GM19099	blood:	n/a	n/a
2	MYC	chr2:74208271-74208394	HepG2	liver:	n/a	n/a
3	POLR2A	chr2:74208262-74208871	K562	blood:	n/a	n/a
4	MAX	chr2:74207961-74209099	HCT-116	colon:	n/a	n/a
5	SIN3AK20	chr2:74208156-74208794	K562	blood:	n/a	n/a
6	POLR2A	chr2:74208343-74208775	H1-hESC	embryonic stem cell:	n/a	n/a
7	MYC	chr2:74208092-74208829	K562	blood:	n/a	n/a
8	MTA3	chr2:74208042-74208602	GM12878	blood:	n/a	n/a
9	MAX	chr2:74208169-74208768	K562	blood:	n/a	n/a
10	POLR2A	chr2:74208029-74208851	K562	blood:	n/a	n/a
11	RCOR1	chr2:74208180-74208974	K562	blood:	n/a	n/a
12	RUNX3	chr2:74208188-74208826	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:74208257-74208954	GM12878	blood:	n/a	n/a
14	CHD2	chr2:74208317-74208732	GM12878	blood:	n/a	n/a
15	MAZ	chr2:74208278-74209012	K562	blood:	n/a	n/a
16	TAF1	chr2:74208342-74208659	H1-hESC	embryonic stem cell:	n/a	n/a
17	CREB1	chr2:74208276-74208642	A549	lung:	n/a	n/a
18	FOS	chr2:74208114-74208401	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr2:74208156-74209055	K562	blood:	n/a	n/a
20	POLR2A	chr2:74208051-74212199	MCF10A-Er-Src	breast:	n/a	n/a
21	SIN3AK20	chr2:74208074-74208894	A549	lung:	n/a	n/a
22	ZBTB33	chr2:74208104-74208922	A549	lung:	n/a	n/a
23	POLR2A	chr2:74208256-74208733	Hela-S3	cervix:	n/a	n/a
24	FOSL2	chr2:74208067-74208724	A549	lung:	n/a	n/a
25	MXI1	chr2:74208226-74209055	H1-hESC	embryonic stem cell:	n/a	n/a
26	BHLHE40	chr2:74208181-74208668	GM12878	blood:	n/a	n/a
27	CBX3	chr2:74207861-74209093	K562	blood:	n/a	n/a
28	TBL1XR1	chr2:74208336-74208866	K562	blood:	n/a	n/a
29	TBP	chr2:74208330-74209080	H1-hESC	embryonic stem cell:	n/a	n/a
30	PML	chr2:74208246-74209135	K562	blood:	n/a	n/a
31	POLR2A	chr2:74208262-74209052	K562	blood:	n/a	n/a
32	POLR2A	chr2:74208166-74208880	GM12892	blood:	n/a	n/a
33	POLR2A	chr2:74208254-74208793	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr2:74208108-74209238	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr2:74208071-74210091	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr2:74208134-74208751	GM12892	blood:	n/a	n/a
37	POLR2A	chr2:74208273-74209195	HUVEC	blood vessel:	n/a	n/a
38	STAT3	chr2:74207937-74208755	MCF10A-Er-Src	breast:	n/a	n/a
39	MXI1	chr2:74208140-74208719	K562	blood:	n/a	n/a
40	CHD2	chr2:74208193-74208909	K562	blood:	n/a	n/a
41	CHD2	chr2:74208356-74208972	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr2:74208238-74208982	K562	blood:	n/a	n/a
43	POLR2A	chr2:74208307-74208872	GM15510	blood:	n/a	n/a
44	POLR2A	chr2:74208251-74208840	GM12878	blood:	n/a	n/a
45	MYC	chr2:74208351-74208376	MCF-7	breast:	n/a	n/a
46	POLR2A	chr2:74208232-74209965	A549	lung:	n/a	n/a
47	POLR2A	chr2:74208261-74208858	GM18505	blood:	n/a	n/a
48	SIN3A	chr2:74208269-74208926	H1-hESC	embryonic stem cell:	n/a	n/a
49	REST	chr2:74208262-74208593	A549	lung:	n/a	n/a
50	CHD2	chr2:74208355-74208725	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74194837..74202788-chr2:74203103..74212249,15	K562	blood:
2	chr2:74187365..74198553-chr2:74205167..74212961,17	MCF-7	breast:
3	chr2:74207001..74208760-chr2:74424534..74426983,2	MCF-7	breast:
4	chr2:74052797..74060455-chr2:74207744..74214705,21	MCF-7	breast:
5	chr2:74208160..74210258-chr2:74374135..74376647,3	MCF-7	breast:
6	chr2:74151695..74161558-chr2:74205273..74215127,19	K562	blood:
7	chr2:74151187..74158039-chr2:74203173..74216266,29	MCF-7	breast:
8	chr2:74206459..74210168-chr2:74373577..74376532,3	K562	blood:
9	chr2:74153687..74156890-chr2:74206451..74210129,3	K562	blood:
10	chr2:74147649..74157677-chr2:74203379..74217813,34	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BOLA3-1	chr2:74208262-74208568	ENSG00000237883.1
2	lnc-BOLA3-1	chr2:74208236-74208560	ENSG00000237883.1
3	lnc-BOLA3-1	chr2:74208262-74208488	ENSG00000237883.1
4	lnc-BOLA3-1	chr2:74208236-74208568	NONHSAT071647
5	lnc-BOLA3-1	chr2:74208236-74208566	NR_104029
6	lnc-BOLA3-1	chr2:74208262-74208566	NR_104030

No data

Variant related genes	Relation type
ENSG00000235499	TF binding region
ENSG00000124356	Chromatin interaction
ENSG00000114956	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000201876	Chromatin interaction
ENSG00000163170	Chromatin interaction
ENSG00000065911	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10166873	0.90[AMR][1000 genomes]
rs10197238	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10201998	0.83[EUR][1000 genomes]
rs10207365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10207954	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10208256	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10496194	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11903339	0.83[EUR][1000 genomes]
rs12328448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272165	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28421442	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4852999	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546883	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6714060	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011177	chr2:74167343-74239905	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv3584956	chr2:74197109-74317135	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Systemic lupus erythematosus	23273568	GWAS catalog

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74198400-74208400	Weak transcription	Aorta	Aorta
2	chr2:74206000-74209800	Enhancers	Lung	lung
3	chr2:74206400-74208400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
4	chr2:74206600-74208400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:74206800-74208400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr2:74206800-74208400	Enhancers	Pancreas	Pancrea
7	chr2:74206800-74208400	Enhancers	Right Ventricle	heart
8	chr2:74206800-74211400	Flanking Active TSS	NHEK	skin
9	chr2:74207000-74208400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:74207000-74208600	Weak transcription	HSMMtube	muscle
11	chr2:74207000-74209000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:74207200-74210600	Weak transcription	Dnd41	blood
13	chr2:74207600-74208400	Flanking Active TSS	K562	blood
14	chr2:74207600-74209000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:74207600-74209000	Enhancers	Spleen	Spleen
16	chr2:74207600-74209200	Flanking Active TSS	Duodenum Mucosa	Duodenum
17	chr2:74207600-74209600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:74207600-74209800	Flanking Active TSS	HMEC	breast
19	chr2:74207800-74208400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr2:74207800-74208600	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr2:74207800-74208800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr2:74207800-74209000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:74207800-74209200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
24	chr2:74207800-74209400	Flanking Bivalent TSS/Enh	HepG2	liver
25	chr2:74207800-74209800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:74208000-74208400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
27	chr2:74208000-74208400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:74208000-74208400	Enhancers	Colon Smooth Muscle	Colon
29	chr2:74208000-74208400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr2:74208000-74208400	Flanking Active TSS	NHDF-Ad	bronchial
31	chr2:74208000-74208600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr2:74208000-74208800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
33	chr2:74208000-74208800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
34	chr2:74208000-74208800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
35	chr2:74208000-74208800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
36	chr2:74208000-74208800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr2:74208000-74208800	Active TSS	Hela-S3	cervix
38	chr2:74208000-74209000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
39	chr2:74208000-74209000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr2:74208000-74209000	Flanking Active TSS	HUVEC	blood vessel
41	chr2:74208000-74209000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr2:74208000-74209200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr2:74208000-74209600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
44	chr2:74208000-74209800	Active TSS	Rectal Smooth Muscle	rectum
45	chr2:74208200-74208400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr2:74208200-74208400	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:74208200-74208400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:74208200-74208400	Flanking Bivalent TSS/Enh	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:74208200-74208400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:74208200-74208400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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