Variant report

Variant	rs1693869
Chromosome Location	chr2:47402064-47402065
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:211)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:211 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47400066-47404709	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr2:47401947-47402299	Hela-S3	cervix:	n/a	n/a
3	CHD2	chr2:47401947-47404355	Hela-S3	cervix:	n/a	chr2:47402298-47402308 chr2:47403103-47403113 chr2:47403143-47403150
4	MAFK	chr2:47401883-47402771	Hela-S3	cervix:	n/a	n/a
5	RAD21	chr2:47396737-47406140	SK-N-SH	brain:	n/a	chr2:47402878-47402891 chr2:47402875-47402894 chr2:47403663-47403673 chr2:47403109-47403119 chr2:47406082-47406094
6	POLR2A	chr2:47401635-47404602	U87	brain:	n/a	n/a
7	BCLAF1	chr2:47401872-47402871	GM12878	blood:	n/a	n/a
8	PBX3	chr2:47401763-47402671	SK-N-SH	brain:	n/a	n/a
9	ZNF263	chr2:47401891-47404452	HEK293-T-REx	kidney:	n/a	chr2:47402297-47402306
10	POLR2A	chr2:47401654-47404707	GM12892	blood:	n/a	n/a
11	TCF7L2	chr2:47401965-47402748	PANC-1	pancreas:	n/a	chr2:47402508-47402515
12	POLR2A	chr2:47396007-47404625	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr2:47382524-47406811	PFSK-1	brain:	n/a	n/a
14	WRNIP1	chr2:47401983-47402710	GM12878	blood:	n/a	n/a
15	TBL1XR1	chr2:47401993-47404757	K562	blood:	n/a	n/a
16	POLR2A	chr2:47401945-47404470	H1-neurons	neurons:	n/a	n/a
17	MAX	chr2:47401904-47402676	ECC-1	luminal epithelium:	n/a	n/a
18	SIN3AK20	chr2:47401971-47403281	K562	blood:	n/a	n/a
19	MXI1	chr2:47400996-47405178	IMR90	lung:	n/a	chr2:47404059-47404074
20	MBD4	chr2:47401766-47402778	HepG2	liver:	n/a	n/a
21	E2F4	chr2:47401921-47402357	MCF10A-Er-Src	breast:	n/a	n/a
22	MAX	chr2:47401722-47404739	A549	lung:	n/a	chr2:47403119-47403128
23	POLR2A	chr2:47382225-47405286	PFSK-1	brain:	n/a	n/a
24	POLR2A	chr2:47399144-47404652	GM12892	blood:	n/a	n/a
25	POLR2A	chr2:47401906-47403826	H1-hESC	embryonic stem cell:	n/a	n/a
26	CHD1	chr2:47401710-47402886	H1-hESC	embryonic stem cell:	n/a	chr2:47402298-47402308
27	ZNF143	chr2:47402051-47402459	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:47401709-47404696	GM12891	blood:	n/a	n/a
29	EBF1	chr2:47402019-47402242	GM12878	blood:	n/a	n/a
30	POLR2A	chr2:47401967-47404465	HL-60	blood:	n/a	n/a
31	ESR1	chr2:47401921-47402401	ECC-1	luminal epithelium:	n/a	n/a
32	TEAD4	chr2:47401977-47402980	K562	blood:	n/a	n/a
33	RUNX3	chr2:47401921-47402557	GM12878	blood:	n/a	n/a
34	MAX	chr2:47402028-47404436	GM12878	blood:	n/a	chr2:47403119-47403128
35	MYBL2	chr2:47401912-47402635	HepG2	liver:	n/a	n/a
36	ETS1	chr2:47401907-47402794	A549	lung:	n/a	chr2:47402298-47402309
37	NR2F2	chr2:47401924-47402924	K562	blood:	n/a	n/a
38	POLR2A	chr2:47401615-47404660	H1-hESC	embryonic stem cell:	n/a	n/a
39	TCF7L2	chr2:47401986-47402787	HEK293	kidney:	n/a	chr2:47402508-47402515
40	POLR2A	chr2:47402046-47402193	A549	lung:	n/a	n/a
41	MAX	chr2:47401771-47404683	A549	lung:	n/a	chr2:47403119-47403128
42	SIN3AK20	chr2:47401381-47402639	A549	lung:	n/a	n/a
43	REST	chr2:47401948-47402919	PFSK-1	brain:	n/a	chr2:47402851-47402871 chr2:47402862-47402882 chr2:47402862-47402882 chr2:47402851-47402871
44	POLR2A	chr2:47401956-47404574	GM12878	blood:	n/a	n/a
45	POLR2A	chr2:47401890-47404650	HL-60	blood:	n/a	n/a
46	ZNF384	chr2:47401952-47404393	K562	blood:	n/a	n/a
47	TBP	chr2:47401910-47402381	Hela-S3	cervix:	n/a	n/a
48	TEAD4	chr2:47401964-47402511	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr2:47401853-47404449	GM12891	blood:	n/a	n/a
50	POLR2A	chr2:47401860-47404601	GM18505	blood:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47220862..47225029-chr2:47401840..47405113,4	K562	blood:
2	chr19:13262402..13265280-chr2:47401781..47403940,2	MCF-7	breast:
3	chr2:47399756..47406251-chr2:47447036..47455846,12	MCF-7	breast:
4	chr2:46655601..46658738-chr2:47401405..47405423,5	K562	blood:
5	chr2:47141013..47143779-chr2:47401317..47404567,3	MCF-7	breast:
6	chr2:47140015..47142222-chr2:47401259..47403402,2	K562	blood:
7	chr2:47399705..47406684-chr2:47448496..47456698,16	K562	blood:
8	chr2:47319263..47321781-chr2:47402053..47403582,2	MCF-7	breast:
9	chr2:47166915..47170495-chr2:47399445..47404516,7	MCF-7	breast:
10	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:
11	chr2:47400478..47403818-chr2:48008752..48011597,4	K562	blood:
12	chr2:47232895..47237077-chr2:47401374..47404385,4	MCF-7	breast:
13	chr1:28835371..28837619-chr2:47401530..47403667,2	K562	blood:
14	chr16:3022787..3025377-chr2:47401877..47403851,2	K562	blood:
15	chr1:45186357..45188685-chr2:47401476..47403610,2	K562	blood:
16	chr2:47399705..47405092-chr2:47450546..47458227,19	K562	blood:
17	chr2:47401421..47404385-chr2:47596204..47598281,3	MCF-7	breast:
18	chr2:47381115..47385095-chr2:47400722..47404896,4	MCF-7	breast:
19	chr2:47401987..47404848-chr2:47628320..47632624,5	MCF-7	breast:
20	chr2:47168040..47171171-chr2:47402063..47404163,4	K562	blood:
21	chr2:47401904..47404708-chr2:47598417..47601115,2	MCF-7	breast:
22	chr2:47401510..47404292-chr3:9438426..9440104,2	K562	blood:
23	chr2:47260087..47265958-chr2:47400378..47404964,8	K562	blood:
24	chr2:38975839..38978922-chr2:47400598..47403972,4	K562	blood:
25	chr2:47140015..47142269-chr2:47400720..47402759,3	K562	blood:
26	chr2:47220711..47222484-chr2:47400487..47403204,2	MCF-7	breast:
27	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
28	chr2:47205588..47209510-chr2:47401817..47405792,7	K562	blood:
29	chr2:47142780..47146808-chr2:47401206..47405117,7	K562	blood:

No data

Variant related genes	Relation type
CALM2	TF binding region
ENSG00000239605	Chromatin interaction
ENSG00000116062	Chromatin interaction
ENSG00000180198	Chromatin interaction
ENSG00000095002	Chromatin interaction
ENSG00000119888	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000206573	Chromatin interaction
ENSG00000187600	Chromatin interaction
ENSG00000226087	Chromatin interaction
ENSG00000267598	Chromatin interaction
ENSG00000168137	Chromatin interaction
ENSG00000127564	Chromatin interaction
ENSG00000160888	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11685529	1.00[CHB][hapmap]
rs1353644	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723482	0.82[JPT][hapmap]
rs1723483	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723484	0.92[CEU][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1723493	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2454081	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs815802	0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs815807	0.92[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs815811	0.89[ASN][1000 genomes]
rs815815	0.92[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs815816	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 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	chr2:47387600-47402200	Weak transcription	Gastric	stomach
2	chr2:47396800-47402600	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr2:47399200-47402400	Flanking Active TSS	Adipose Nuclei	Adipose
4	chr2:47399200-47404400	Active TSS	HSMMtube	muscle
5	chr2:47399400-47402600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:47399400-47402600	Transcr. at gene 5' and 3'	K562	blood
7	chr2:47399800-47402200	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr2:47399800-47402600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:47399800-47404200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:47399800-47404400	Active TSS	Stomach Smooth Muscle	stomach
11	chr2:47400000-47402200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr2:47400000-47402200	Flanking Active TSS	HUVEC	blood vessel
13	chr2:47400000-47403000	Active TSS	Right Atrium	heart
14	chr2:47400000-47404000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:47400000-47404600	Active TSS	Psoas Muscle	Psoas
16	chr2:47400200-47402200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr2:47400200-47402600	Transcr. at gene 5' and 3'	NHEK	skin
18	chr2:47400400-47402400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr2:47400400-47405200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:47400600-47402400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr2:47400600-47404600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr2:47400800-47403200	Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr2:47400800-47404000	Active TSS	NH-A	brain
24	chr2:47400800-47404400	Active TSS	ES-I3 Cell Line	embryonic stem cell
25	chr2:47400800-47404400	Active TSS	Fetal Intestine Small	intestine
26	chr2:47400800-47404400	Active TSS	Ovary	ovary
27	chr2:47401000-47402200	Flanking Active TSS	Liver	Liver
28	chr2:47401000-47403200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
29	chr2:47401000-47403400	Active TSS	Aorta	Aorta
30	chr2:47401000-47404000	Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr2:47401000-47404000	Active TSS	HMEC	breast
32	chr2:47401000-47404200	Active TSS	H1 Cell Line	embryonic stem cell
33	chr2:47401000-47404200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:47401000-47404200	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr2:47401000-47404200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:47401000-47404200	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr2:47401000-47404200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr2:47401000-47404200	Active TSS	Duodenum Mucosa	Duodenum
39	chr2:47401000-47404200	Active TSS	Fetal Intestine Large	intestine
40	chr2:47401000-47404200	Active TSS	Rectal Smooth Muscle	rectum
41	chr2:47401000-47404200	Active TSS	NHDF-Ad	bronchial
42	chr2:47401000-47404400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:47401000-47404400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:47401000-47404400	Active TSS	Brain Anterior Caudate	brain
45	chr2:47401000-47404400	Active TSS	Brain Hippocampus Middle	brain
46	chr2:47401000-47404400	Active TSS	Fetal Brain Female	brain
47	chr2:47401000-47404400	Active TSS	Fetal Kidney	kidney
48	chr2:47401000-47404400	Active TSS	GM12878-XiMat	blood
49	chr2:47401000-47404600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr2:47401000-47404600	Active TSS	Right Ventricle	heart

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