Variant report

Variant	rs6519802
Chromosome Location	chr22:30476271-30476272
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr22:30476091-30476707	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr22:30476058-30476291	H1-hESC	embryonic stem cell:	n/a	n/a
3	POU2F2	chr22:30476019-30476561	GM12878	blood:	n/a	n/a
4	TBP	chr22:30476112-30476613	H1-hESC	embryonic stem cell:	n/a	n/a
5	POU5F1	chr22:30476056-30476560	H1-hESC	embryonic stem cell:	n/a	n/a
6	NANOG	chr22:30475996-30476522	H1-hESC	embryonic stem cell:	n/a	n/a
7	JUND	chr22:30476223-30476546	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F6	chr22:30476066-30476864	H1-hESC	embryonic stem cell:	n/a	chr22:30476599-30476608
9	CHD2	chr22:30476208-30476527	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr22:30476054-30476731	H1-hESC	embryonic stem cell:	n/a	n/a
11	POU2F2	chr22:30476192-30476544	GM12891	blood:	n/a	n/a
12	POLR2A	chr22:30475991-30476719	H1-hESC	embryonic stem cell:	n/a	n/a
13	RAD21	chr22:30476025-30476365	H1-hESC	embryonic stem cell:	n/a	n/a
14	SP1	chr22:30476060-30476646	H1-hESC	embryonic stem cell:	n/a	chr22:30476376-30476387
15	E2F6	chr22:30476053-30476683	H1-hESC	embryonic stem cell:	n/a	chr22:30476599-30476608
16	MAX	chr22:30476190-30476707	H1-hESC	embryonic stem cell:	n/a	n/a
17	POU5F1	chr22:30476134-30476453	H1-hESC	embryonic stem cell:	n/a	n/a
18	POU2F2	chr22:30476170-30476494	GM12878	blood:	n/a	n/a
19	POLR2A	chr22:30476076-30476305	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF1	chr22:30476048-30476604	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr22:30476254-30476304	Hepatocyte	liver:	n/a
2	chr22:30476254-30476304	NT2-D1	testis:	n/a
3	chr22:30476254-30476304	BE2_C	brain:	n/a
4	chr22:30476254-30476304	ProgFib	skin:	n/a
5	chr22:30476254-30476304	HCF	heart:	n/a
6	chr22:30476254-30476304	CMK	blood:	n/a
7	chr22:30476254-30476304	HAEpiC	amniotic membrane:	n/a
8	chr22:30476254-30476304	AG04450	lung:	fetal
9	chr22:30476254-30476304	HIPEpiC	eye:	n/a
10	chr22:30476254-30476304	LNCaP	prostate:	n/a
11	chr22:30476254-30476304	A549	lung:	n/a
12	chr22:30476254-30476304	HRE	kidney:	n/a
13	chr22:30476254-30476304	GM12892	blood:	n/a
14	chr22:30476254-30476304	HEEpiC	esophagus:	n/a
15	chr22:30476254-30476304	NHDF-neo	bronchial:	n/a
16	chr22:30476254-30476304	AG09319	gingival:	n/a
17	chr22:30476254-30476304	U87	brain:	n/a
18	chr22:30476254-30476304	GM12891	blood:	n/a
19	chr22:30476254-30476304	HCT-116	colon:	n/a
20	chr22:30476254-30476304	GM19239	blood:	n/a
21	chr22:30476254-30476304	NH-A	brain:	n/a
22	chr22:30476254-30476304	ovcar-3	ovarian:	n/a
23	chr22:30476254-30476304	PrEC	prostate:	n/a
24	chr22:30476254-30476304	HMEC	breast:	n/a
25	chr22:30476254-30476304	SK-N-SH	brain:	n/a
26	chr22:30476254-30476304	SK-N-MC	brain:	n/a
27	chr22:30476254-30476304	AG10803	skin:	n/a
28	chr22:30476254-30476304	GM06990	blood:	n/a
29	chr22:30476254-30476304	Caco-2	colon:	n/a
30	chr22:30476254-30476304	HPAEpiC	pulmonary alveolar:	n/a
31	chr22:30476254-30476304	HepG2	liver:	n/a
32	chr22:30476254-30476304	HCPEpiC	choroid plexus:	n/a
33	chr22:30476254-30476304	HNPCEpiC	eye:	n/a
34	chr22:30476254-30476304	HCM	heart:	n/a
35	chr22:30476254-30476304	NHBE	bronchial:	n/a
36	chr22:30476254-30476304	MCF-7	breast:	n/a
37	chr22:30476254-30476304	SAEC	small airway:	n/a
38	chr22:30476254-30476304	Jurkat	blood:	n/a
39	chr22:30476254-30476304	ECC-1	luminal epithelium:	n/a
40	chr22:30476254-30476304	AoSMC	blood vessel:	n/a
41	chr22:30476254-30476304	HRPEpiC	eye:	n/a
42	chr22:30476254-30476304	PANC-1	pancreas:	n/a
43	chr22:30476254-30476304	BJ	skin:	n/a
44	chr22:30476254-30476304	AG09309	skin:	n/a
45	chr22:30476254-30476304	HEK293	kidney:	embryo
46	chr22:30476254-30476304	PFSK-1	brain:	n/a
47	chr22:30476254-30476304	SK-N-SH_RA	brain:	n/a
48	chr22:30476254-30476304	RPTEC	kidney:	n/a
49	chr22:30476254-30476304	K562	blood:	n/a
50	chr22:30476254-30476304	T-47D	breast:	n/a

No data

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIF-2	chr22:30476117-30476469	ENSG00000227117.2
2	lnc-LIF-2	chr22:30476117-30476427	ENSG00000227117.2
3	lnc-LIF-2	chr22:30476117-30476884	NONHSAT084754
4	lnc-LIF-2	chr22:30476117-30476884	NONHSAT084756
5	lnc-LIF-2	chr22:30476117-30476469	NR_110541

No data

Variant related genes	Relation type
ENSG00000227117	TF binding region
HORMAD2	TF binding region
ENSG00000227117	CpG island
HORMAD2	CpG island

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11552852	0.84[EUR][1000 genomes]
rs1544429	0.80[EUR][1000 genomes]
rs1544431	1.00[YRI][hapmap]
rs16988143	0.94[YRI][hapmap];0.83[AFR][1000 genomes]
rs16988148	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs16988149	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs16988244	1.00[ASW][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988291	0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988303	0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988304	1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988333	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17648208	0.91[EUR][1000 genomes]
rs1807726	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412980	0.92[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs2412981	0.87[EUR][1000 genomes]
rs36608	0.84[EUR][1000 genomes]
rs41278853	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41281623	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41281633	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4482600	0.87[EUR][1000 genomes]
rs4482601	0.84[EUR][1000 genomes]
rs45629133	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4820823	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4823078	0.87[EUR][1000 genomes]
rs55645000	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56392746	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56406718	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5752979	0.80[EUR][1000 genomes]
rs5753038	0.80[EUR][1000 genomes]
rs5753039	0.87[EUR][1000 genomes]
rs5753042	0.87[EUR][1000 genomes]
rs5753043	0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs5763855	0.87[EUR][1000 genomes]
rs5763856	0.87[EUR][1000 genomes]
rs5763857	0.87[EUR][1000 genomes]
rs5763858	0.87[EUR][1000 genomes]
rs5763870	0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs5763873	0.87[EUR][1000 genomes]
rs5763878	0.87[YRI][hapmap];0.87[EUR][1000 genomes]
rs58162368	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997597	0.85[MEX][hapmap];0.83[TSI][hapmap]
rs6006383	0.87[EUR][1000 genomes]
rs60759987	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6518681	0.87[EUR][1000 genomes]
rs6519805	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs713916	0.81[YRI][hapmap];0.87[EUR][1000 genomes]
rs7284951	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7285585	0.87[EUR][1000 genomes]
rs7286205	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7287233	0.83[AFR][1000 genomes]
rs7290175	0.87[EUR][1000 genomes]
rs737901	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883349	0.83[AFR][1000 genomes]
rs73883354	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73883355	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73883359	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73883360	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883363	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883367	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883370	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883374	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883375	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883377	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883378	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8141471	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs962322	0.81[YRI][hapmap];0.87[EUR][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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30473400-30476400	Weak transcription	Fetal Lung	lung
2	chr22:30474400-30476600	Weak transcription	HepG2	liver
3	chr22:30475200-30476600	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr22:30475400-30476600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr22:30475400-30476600	Enhancers	Fetal Brain Male	brain
6	chr22:30475600-30476600	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr22:30475800-30476400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr22:30475800-30476400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr22:30475800-30476600	Active TSS	H1 Cell Line	embryonic stem cell
10	chr22:30475800-30476600	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr22:30475800-30476600	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr22:30475800-30476600	Bivalent/Poised TSS	Placenta	Placenta
13	chr22:30475800-30476800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr22:30475800-30476800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:30475800-30485400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr22:30476000-30476400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr22:30476000-30476400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr22:30476000-30476400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr22:30476000-30476400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr22:30476000-30476400	Active TSS	Brain Angular Gyrus	brain
21	chr22:30476000-30476400	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr22:30476000-30476400	Flanking Active TSS	GM12878-XiMat	blood
23	chr22:30476000-30476400	Active TSS	HUVEC	blood vessel
24	chr22:30476000-30476400	Active TSS	NH-A	brain
25	chr22:30476000-30476600	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr22:30476000-30476600	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr22:30476000-30476600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
29	chr22:30476000-30476600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr22:30476000-30476600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr22:30476000-30476600	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr22:30476000-30476600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
35	chr22:30476000-30476600	Active TSS	Psoas Muscle	Psoas
36	chr22:30476000-30476600	Active TSS	Right Atrium	heart
37	chr22:30476000-30476600	Active TSS	Right Ventricle	heart
38	chr22:30476000-30476600	Enhancers	Spleen	Spleen
39	chr22:30476000-30476600	Active TSS	Osteobl	bone
40	chr22:30476000-30476800	Active TSS	Brain Anterior Caudate	brain
41	chr22:30476000-30476800	Active TSS	Brain Germinal Matrix	brain
42	chr22:30476000-30476800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
43	chr22:30476000-30476800	Active TSS	Fetal Brain Female	brain
44	chr22:30476000-30477200	Active TSS	Brain Substantia Nigra	brain
45	chr22:30476200-30476400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr22:30476200-30476400	Active TSS	Primary B cells from cord blood	blood
47	chr22:30476200-30476400	Active TSS	Muscle Satellite Cultured Cells	--
48	chr22:30476200-30476400	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
49	chr22:30476200-30476400	Flanking Active TSS	Fetal Intestine Large	intestine
50	chr22:30476200-30476400	Bivalent/Poised TSS	Fetal Muscle Leg	muscle

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