Variant report

Variant	rs6742975
Chromosome Location	chr2:231276524-231276525
allele	A/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	POLR2A	chr2:231276348-231276540	A549	lung:	n/a	n/a
2	STAT2	chr2:231276417-231276814	K562	blood:	n/a	chr2:231276625-231276636 chr2:231276622-231276637
3	POLR2A	chr2:231276445-231276920	A549	lung:	n/a	n/a
4	REST	chr2:231276261-231277024	A549	lung:	n/a	chr2:231277008-231277022
5	POLR2A	chr2:231276513-231276902	HUVEC	blood vessel:	n/a	n/a
6	IRF1	chr2:231276437-231276817	K562	blood:	n/a	chr2:231276624-231276635 chr2:231276619-231276632 chr2:231276619-231276632 chr2:231276625-231276638 chr2:231276620-231276641 chr2:231276618-231276638 chr2:231276619-231276632 chr2:231276625-231276639 chr2:231276625-231276638 chr2:231276626-231276640 chr2:231276620-231276634 chr2:231276613-231276629 chr2:231276624-231276638 chr2:231276626-231276636 chr2:231276619-231276632 chr2:231276619-231276633 chr2:231276622-231276636
7	POLR2A	chr2:231276231-231276903	Hela-S3	cervix:	n/a	n/a
8	STAT1	chr2:231276089-231276885	GM12878	blood:	n/a	chr2:231276625-231276636
9	POLR2A	chr2:231275889-231276994	GM19099	blood:	n/a	n/a
10	POLR2A	chr2:231276157-231276981	U87	brain:	n/a	n/a
11	MYC	chr2:231276422-231276925	K562	blood:	n/a	n/a
12	POLR2A	chr2:231276169-231277041	GM12878	blood:	n/a	n/a
13	MAX	chr2:231275762-231277128	HepG2	liver:	n/a	n/a
14	YY1	chr2:231276253-231277057	HepG2	liver:	n/a	n/a
15	TBP	chr2:231276371-231276710	Hela-S3	cervix:	n/a	n/a
16	MAZ	chr2:231276249-231276903	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr2:231276187-231277060	GM12892	blood:	n/a	n/a
18	MAZ	chr2:231276409-231276878	GM12878	blood:	n/a	n/a
19	POLR2A	chr2:231276400-231277027	GM12891	blood:	n/a	n/a
20	POLR2A	chr2:231276364-231276875	PANC-1	pancreas:	n/a	n/a
21	CTCF	chr2:231276500-231276650	SK-N-SH_RA	brain:	n/a	n/a
22	YY1	chr2:231276483-231276811	SK-N-SH_RA	brain:	n/a	n/a
23	PML	chr2:231275893-231277239	GM12878	blood:	n/a	n/a
24	MAX	chr2:231276456-231277011	SK-N-SH	brain:	n/a	n/a
25	CHD2	chr2:231276136-231277122	Hela-S3	cervix:	n/a	n/a
26	CTCF	chr2:231276420-231276570	GM12869	blood:	n/a	n/a
27	WRNIP1	chr2:231276456-231276765	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:231276157-231276950	U87	brain:	n/a	n/a
29	POLR2A	chr2:231276234-231276972	Hela-S3	cervix:	n/a	n/a
30	UBTF	chr2:231276223-231277086	K562	blood:	n/a	n/a
31	POLR2A	chr2:231276282-231277085	Gliobla	brain:	n/a	n/a
32	POLR2A	chr2:231276352-231276573	H1-hESC	embryonic stem cell:	n/a	n/a
33	RAD21	chr2:231276311-231276616	H1-hESC	embryonic stem cell:	n/a	n/a
34	RFX5	chr2:231276420-231276939	HepG2	liver:	n/a	chr2:231276895-231276908
35	IRF1	chr2:231276384-231277025	K562	blood:	n/a	chr2:231276624-231276635 chr2:231276619-231276632 chr2:231276619-231276632 chr2:231276625-231276638 chr2:231276620-231276641 chr2:231276618-231276638 chr2:231276619-231276632 chr2:231276625-231276639 chr2:231276625-231276638 chr2:231276626-231276640 chr2:231276620-231276634 chr2:231276613-231276629 chr2:231276624-231276638 chr2:231276626-231276636 chr2:231276619-231276632 chr2:231276619-231276633 chr2:231276622-231276636
36	HA-E2F1	chr2:231276515-231276967	Hela-S3	cervix:	n/a	n/a
37	HEY1	chr2:231276204-231277033	HepG2	liver:	n/a	n/a
38	CTCF	chr2:231276400-231276550	GM06990	blood:	n/a	n/a
39	POLR2A	chr2:231276363-231276951	K562	blood:	n/a	n/a
40	HEY1	chr2:231276251-231276956	K562	blood:	n/a	n/a
41	CTCF	chr2:231276520-231276670	HCM	heart:	n/a	n/a
42	SIN3A	chr2:231276423-231276716	GM12878	blood:	n/a	n/a
43	MYC	chr2:231276177-231277032	NB4	blood:	n/a	n/a
44	POLR2A	chr2:231276165-231276982	HepG2	liver:	n/a	n/a
45	POLR2A	chr2:231276124-231276977	GM12892	blood:	n/a	n/a
46	POLR2A	chr2:231276294-231276929	HUVEC	blood vessel:	n/a	n/a
47	NFIC	chr2:231276043-231276999	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr2:231276484-231277035	PANC-1	pancreas:	n/a	n/a
49	ELF1	chr2:231275676-231276566	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:231276458-231276845	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:231276297..231278950-chr2:231279090..231280823,2	MCF-7	breast:
2	chr2:231187646..231188478-chr2:231276184..231277085,2	HCT-116	colon:
3	chr2:231269734..231271710-chr2:231274995..231278115,3	K562	blood:
4	chr1:207495007..207495512-chr2:231276404..231277158,2	NB4	blood:
5	chr2:231276390..231278062-chr2:231285132..231287454,2	K562	blood:
6	chr2:231276236..231278325-chr2:231279653..231283011,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-6	chr2:231275415-231277244	NONHSAT077283

Variant related genes	Relation type
SP100	TF binding region
ENSG00000196352	Chromatin interaction
ENSG00000067066	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10933334	0.91[EUR][1000 genomes]
rs10933336	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11688808	0.91[EUR][1000 genomes]
rs11902383	0.91[EUR][1000 genomes]
rs12104570	0.91[EUR][1000 genomes]
rs12694857	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1582830	0.89[EUR][1000 genomes]
rs1820550	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1968340	0.91[EUR][1000 genomes]
rs1968341	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs3845827	0.95[CEU][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6436929	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs6436932	0.95[CEU][hapmap];0.81[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6436935	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6707728	0.98[EUR][1000 genomes]
rs6717687	0.94[EUR][1000 genomes]
rs6728619	0.95[CEU][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs6731825	0.98[EUR][1000 genomes]
rs6737808	0.95[CEU][hapmap];0.81[JPT][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6741595	0.97[EUR][1000 genomes]
rs6746556	0.98[EUR][1000 genomes]
rs7563493	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7607380	0.91[EUR][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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv2751844	chr2:231179495-231280495	Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv875946	chr2:231184106-231277567	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875947	chr2:231190446-231281286	Weak transcription Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv521344	chr2:231267925-231281286	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv584671	chr2:231273229-231284556	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 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	chr2:231275600-231277000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr2:231275600-231277200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr2:231275600-231277400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:231275800-231276800	Active TSS	NH-A	brain
5	chr2:231275800-231277000	Active TSS	Primary T cells from cord blood	blood
6	chr2:231275800-231277000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:231275800-231277200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr2:231275800-231277200	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr2:231275800-231277200	Active TSS	A549	lung
10	chr2:231276000-231276600	Flanking Active TSS	NHEK	skin
11	chr2:231276000-231276800	Active TSS	Primary hematopoietic stem cells	blood
12	chr2:231276000-231276800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
13	chr2:231276000-231276800	Active TSS	Brain Hippocampus Middle	brain
14	chr2:231276000-231277000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr2:231276000-231277000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:231276000-231277000	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr2:231276000-231277000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
18	chr2:231276000-231277000	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr2:231276000-231277000	Active TSS	Brain Germinal Matrix	brain
20	chr2:231276000-231277000	Active TSS	Brain Substantia Nigra	brain
21	chr2:231276000-231277000	Active TSS	Esophagus	oesophagus
22	chr2:231276000-231277000	Active TSS	Left Ventricle	heart
23	chr2:231276000-231277000	Active TSS	Lung	lung
24	chr2:231276000-231277200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
25	chr2:231276000-231277200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr2:231276000-231277200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
27	chr2:231276000-231277200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr2:231276000-231277200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:231276000-231277200	Active TSS	Aorta	Aorta
30	chr2:231276000-231277200	Active TSS	Brain Anterior Caudate	brain
31	chr2:231276000-231277200	Active TSS	Fetal Kidney	kidney
32	chr2:231276000-231277200	Active TSS	Gastric	stomach
33	chr2:231276000-231277200	Active TSS	Ovary	ovary
34	chr2:231276000-231277200	Active TSS	Psoas Muscle	Psoas
35	chr2:231276000-231277400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:231276000-231277400	Active TSS	Brain Cingulate Gyrus	brain
37	chr2:231276000-231277600	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr2:231276000-231277600	Active TSS	Rectal Smooth Muscle	rectum
39	chr2:231276200-231276600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
40	chr2:231276200-231276800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr2:231276200-231276800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:231276200-231276800	Active TSS	Primary T cells fromperipheralblood	blood
43	chr2:231276200-231276800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:231276200-231276800	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr2:231276200-231276800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr2:231276200-231276800	Active TSS	Fetal Lung	lung
47	chr2:231276200-231276800	Active TSS	Pancreas	Pancrea
48	chr2:231276200-231276800	Active TSS	Rectal Mucosa Donor 31	rectum
49	chr2:231276200-231277000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr2:231276200-231277000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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