Variant report

Variant	rs2159200
Chromosome Location	chr2:234777209-234777210
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:70)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:70 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:234776748-234777244	GM18505	blood:	n/a	n/a
2	BRCA1	chr2:234776797-234777276	Hela-S3	cervix:	n/a	n/a
3	MAX	chr2:234776509-234777363	A549	lung:	n/a	n/a
4	MYC	chr2:234776649-234777214	K562	blood:	n/a	n/a
5	TCF7L2	chr2:234776763-234777219	PANC-1	pancreas:	n/a	n/a
6	E2F6	chr2:234776514-234777268	A549	lung:	n/a	n/a
7	POLR2A	chr2:234776562-234777333	PFSK-1	brain:	n/a	n/a
8	CREB1	chr2:234776675-234777244	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr2:234776622-234777245	MCF-7	breast:	n/a	n/a
10	CREB1	chr2:234776679-234777354	K562	blood:	n/a	n/a
11	E2F4	chr2:234776999-234777221	MCF10A-Er-Src	breast:	n/a	n/a
12	TCF12	chr2:234776467-234777327	A549	lung:	n/a	n/a
13	POLR2A	chr2:234776642-234777245	GM12891	blood:	n/a	n/a
14	POLR2A	chr2:234776652-234777251	HCT-116	colon:	n/a	n/a
15	MAX	chr2:234776380-234777363	A549	lung:	n/a	n/a
16	TBP	chr2:234776944-234777262	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr2:234776733-234777226	K562	blood:	n/a	n/a
18	CTCF	chr2:234776949-234777430	K562	blood:	n/a	n/a
19	POLR2A	chr2:234776600-234777274	HCT-116	colon:	n/a	n/a
20	IRF1	chr2:234776791-234777265	K562	blood:	n/a	n/a
21	GTF2F1	chr2:234776659-234777239	Hela-S3	cervix:	n/a	n/a
22	EGR1	chr2:234776310-234777291	HCT-116	colon:	n/a	n/a
23	HA-E2F1	chr2:234776681-234777372	MCF-7	breast:	n/a	n/a
24	HCFC1	chr2:234776610-234777497	Hela-S3	cervix:	n/a	n/a
25	E2F6	chr2:234776455-234777243	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr2:234776696-234777247	GM19193	blood:	n/a	n/a
27	RCOR1	chr2:234776683-234777275	K562	blood:	n/a	n/a
28	JUN	chr2:234776514-234777472	K562	blood:	n/a	n/a
29	ATF1	chr2:234776839-234777223	K562	blood:	n/a	n/a
30	POLR2A	chr2:234776542-234777342	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr2:234776743-234777216	GM12891	blood:	n/a	n/a
32	POLR2A	chr2:234776691-234777248	MCF-7	breast:	n/a	n/a
33	POLR2A	chr2:234776663-234777239	A549	lung:	n/a	n/a
34	CREB1	chr2:234776840-234777222	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr2:234776760-234777266	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr2:234776474-234777250	MCF-7	breast:	n/a	n/a
37	CREB1	chr2:234776714-234777283	K562	blood:	n/a	n/a
38	POLR2A	chr2:234776687-234777274	HUVEC	blood vessel:	n/a	n/a
39	POLR2A	chr2:234776734-234777237	GM18951	blood:	n/a	n/a
40	POLR2A	chr2:234776823-234777289	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F6	chr2:234776535-234777217	K562	blood:	n/a	n/a
42	E2F6	chr2:234776553-234777233	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr2:234776756-234777252	GM12878	blood:	n/a	n/a
44	E2F6	chr2:234776456-234777363	A549	lung:	n/a	n/a
45	ARID3A	chr2:234777010-234777379	K562	blood:	n/a	n/a
46	NRF1	chr2:234776787-234777440	SK-N-SH	brain:	n/a	n/a
47	BCLAF1	chr2:234776791-234777246	GM12878	blood:	n/a	n/a
48	MYC	chr2:234776586-234777223	K562	blood:	n/a	n/a
49	POLR2A	chr2:234776733-234777283	GM12891	blood:	n/a	n/a
50	TCF7L2	chr2:234776718-234777212	HCT-116	colon:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:234775602..234777791-chr7:117824084..117825749,2	MCF-7	breast:
2	2:234635414-234639782..2:234772667-234780240	Hela-S3	cervix:
3	2:234683624-234705119..2:234772667-234780240	Hela-S3	cervix:
4	2:234772667-234780240..2:234954947-234965240	Hela-S3	cervix:
5	2:234543708-234558325..2:234772667-234780240	Hela-S3	cervix:

No data

Variant related genes	Relation type
MSL3P1	TF binding region
ENSG00000243135	Chromatin interaction
ENSG00000185038	Chromatin interaction
ENSG00000234143	Chromatin interaction
ENSG00000072080	Chromatin interaction
ENSG00000128534	Chromatin interaction
ENSG00000241635	Chromatin interaction
ENSG00000242515	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1003540	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10166942	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10170399	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10187654	0.95[ASN][1000 genomes]
rs10929309	0.89[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10929312	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10929314	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11563063	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11563066	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11563227	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11892538	0.84[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12997802	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13016127	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13016553	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1392606	0.92[CEU][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1965629	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1985366	0.91[ASN][1000 genomes]
rs2286430	0.89[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2286431	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2302155	0.89[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2362290	0.83[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs3732215	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4233636	0.82[ASN][1000 genomes]
rs4663983	0.92[ASN][1000 genomes]
rs4663986	0.82[ASN][1000 genomes]
rs6431648	0.83[ASN][1000 genomes]
rs6709005	0.84[CHB][hapmap];0.95[JPT][hapmap]
rs6738979	0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs6760630	0.95[ASN][1000 genomes]
rs737636	0.83[ASN][1000 genomes]
rs7567475	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7604471	0.82[ASN][1000 genomes]
rs887061	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917432	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs917433	0.86[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs917434	0.89[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs968402	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs990418	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];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	nsv1013712	chr2:234558457-235495825	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532476	chr2:234595695-235134381	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234775200-234777400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:234776000-234777400	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr2:234776000-234777400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr2:234776000-234777400	Active TSS	A549	lung
5	chr2:234776000-234777400	Active TSS	K562	blood
6	chr2:234776200-234777400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:234776400-234777400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr2:234776400-234777400	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr2:234776400-234777400	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr2:234776400-234777400	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr2:234776400-234777400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr2:234776400-234777400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr2:234776400-234777400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:234776400-234777600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:234776400-234777600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:234776400-234777600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:234776600-234777400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:234776600-234777400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr2:234776600-234777400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:234776600-234777400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
21	chr2:234776600-234777400	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr2:234776600-234777400	Active TSS	Muscle Satellite Cultured Cells	--
23	chr2:234776600-234777400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:234776600-234777400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr2:234776600-234777400	Active TSS	Brain Anterior Caudate	brain
26	chr2:234776600-234777400	Active TSS	Brain Germinal Matrix	brain
27	chr2:234776600-234777400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
28	chr2:234776600-234777400	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr2:234776600-234777400	Active TSS	Duodenum Mucosa	Duodenum
30	chr2:234776600-234777400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:234776600-234777400	Active TSS	Fetal Brain Female	brain
32	chr2:234776600-234777400	Active TSS	Fetal Lung	lung
33	chr2:234776600-234777400	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr2:234776600-234777400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
35	chr2:234776600-234777400	Active TSS	Stomach Smooth Muscle	stomach
36	chr2:234776600-234777400	Active TSS	GM12878-XiMat	blood
37	chr2:234776600-234777400	Active TSS	HMEC	breast
38	chr2:234776600-234777400	Active TSS	HSMMtube	muscle
39	chr2:234776600-234777400	Flanking Active TSS	HUVEC	blood vessel
40	chr2:234776600-234777400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
41	chr2:234776600-234777400	Active TSS	NHDF-Ad	bronchial
42	chr2:234776600-234777400	Active TSS	NHLF	lung
43	chr2:234776600-234777800	Active TSS	Fetal Kidney	kidney
44	chr2:234776800-234777400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr2:234776800-234777400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr2:234776800-234777400	Active TSS	Primary T cells from cord blood	blood
47	chr2:234776800-234777400	Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr2:234776800-234777400	Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr2:234776800-234777400	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr2:234776800-234777400	Active TSS	HSMM	muscle

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