Variant report

Variant	rs6544938
Chromosome Location	chr2:47143187-47143188
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:388)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:388 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr2:47142924-47143259	GM12892	blood:	n/a	n/a
2	SIN3AK20	chr2:47142957-47143628	K562	blood:	n/a	n/a
3	TBP	chr2:47142720-47143580	K562	blood:	n/a	n/a
4	CREB1	chr2:47142852-47143360	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr2:47142731-47143525	GM12892	blood:	n/a	n/a
6	YY1	chr2:47142940-47143479	GM12878	blood:	n/a	n/a
7	UBTF	chr2:47142320-47143616	K562	blood:	n/a	n/a
8	POLR2A	chr2:47142168-47143663	K562	blood:	n/a	n/a
9	ELF1	chr2:47142309-47143520	GM12878	blood:	n/a	chr2:47143079-47143091
10	NFIC	chr2:47142701-47143686	HepG2	liver:	n/a	n/a
11	CREB1	chr2:47142638-47143562	H1-hESC	embryonic stem cell:	n/a	n/a
12	NRF1	chr2:47142826-47143481	GM12878	blood:	n/a	n/a
13	POLR2A	chr2:47142286-47143714	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr2:47142953-47143503	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr2:47142730-47143401	GM10847	blood:	n/a	n/a
16	GABPA	chr2:47142785-47143845	SK-N-SH	brain:	n/a	n/a
17	MBD4	chr2:47142883-47143815	HepG2	liver:	n/a	n/a
18	MAX	chr2:47142661-47143558	Hela-S3	cervix:	n/a	n/a
19	MAX	chr2:47142368-47143610	K562	blood:	n/a	n/a
20	BACH1	chr2:47143005-47143541	H1-hESC	embryonic stem cell:	n/a	n/a
21	FOXM1	chr2:47142914-47143527	GM12878	blood:	n/a	n/a
22	POLR2A	chr2:47141959-47143510	K562	blood:	n/a	n/a
23	MAX	chr2:47142794-47143705	ECC-1	luminal epithelium:	n/a	n/a
24	POLR2A	chr2:47142679-47143622	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr2:47142480-47143924	SK-N-MC	brain:	n/a	n/a
26	CEBPD	chr2:47142715-47143491	HepG2	liver:	n/a	n/a
27	POLR2A	chr2:47142714-47143523	GM15510	blood:	n/a	n/a
28	GTF2F1	chr2:47143040-47143596	Hela-S3	cervix:	n/a	n/a
29	EP300	chr2:47142914-47143309	H1-hESC	embryonic stem cell:	n/a	n/a
30	CHD2	chr2:47142982-47143485	K562	blood:	n/a	n/a
31	POLR2A	chr2:47142682-47143559	HCT-116	colon:	n/a	n/a
32	POLR2A	chr2:47142733-47143755	K562	blood:	n/a	n/a
33	CHD2	chr2:47143021-47143343	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr2:47142367-47144089	HepG2	liver:	n/a	n/a
35	POLR2A	chr2:47142436-47143578	ProgFib	skin:	n/a	n/a
36	YY1	chr2:47142957-47143377	GM12878	blood:	n/a	n/a
37	MYC	chr2:47142918-47143729	A549	lung:	n/a	n/a
38	NFYB	chr2:47142905-47143216	K562	blood:	n/a	n/a
39	ZC3H11A	chr2:47143058-47143467	K562	blood:	n/a	n/a
40	ELF1	chr2:47143006-47143420	K562	blood:	n/a	chr2:47143079-47143091
41	SRF	chr2:47143064-47143334	K562	blood:	n/a	n/a
42	POLR2A	chr2:47142968-47143391	GM12891	blood:	n/a	n/a
43	SIN3AK20	chr2:47142473-47143830	MCF-7	breast:	n/a	n/a
44	MAX	chr2:47142003-47143724	HepG2	liver:	n/a	n/a
45	REST	chr2:47142962-47143252	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr2:47142744-47143358	A549	lung:	n/a	n/a
47	RCOR1	chr2:47142216-47143625	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr2:47142276-47143590	Hela-S3	cervix:	n/a	n/a
49	ELK4	chr2:47142964-47143514	Hela-S3	cervix:	n/a	chr2:47143199-47143210
50	HDAC2	chr2:47142432-47143628	HepG2	liver:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47142780..47146808-chr2:47401206..47405117,7	K562	blood:
2	chr14:75745342..75745895-chr2:47142870..47143556,2	Hela-S3	cervix:
3	chr2:47141013..47143779-chr2:47401317..47404567,3	MCF-7	breast:
4	chr2:47140743..47148534-chr2:47401019..47406419,10	MCF-7	breast:
5	chr2:47139463..47143529-chr2:47167839..47169953,4	K562	blood:
6	chr2:47139886..47146981-chr2:47165365..47170438,17	MCF-7	breast:
7	chr2:47142749..47143262-chr9:33167300..33168060,2	NB4	blood:
8	chr14:94546995..94547498-chr2:47142627..47143331,2	Hela-S3	cervix:
9	chr2:47141557..47143529-chr2:47167839..47169788,2	K562	blood:

No data

Variant related genes	Relation type
TTC7A	TF binding region
MCFD2	TF binding region
ENSG00000086062	Chromatin interaction
ENSG00000170345	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000180398	Chromatin interaction
ENSG00000089737	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10174894	0.98[ASN][1000 genomes]
rs10190862	0.84[EUR][1000 genomes]
rs10190882	0.84[EUR][1000 genomes]
rs10197474	0.84[EUR][1000 genomes]
rs10199965	0.92[ASN][1000 genomes]
rs11890177	0.92[ASN][1000 genomes]
rs11894319	0.98[ASN][1000 genomes]
rs13388612	0.98[ASN][1000 genomes]
rs13392448	0.93[ASN][1000 genomes]
rs13394007	0.84[EUR][1000 genomes]
rs13398851	0.85[ASN][1000 genomes]
rs13410702	0.84[EUR][1000 genomes]
rs13415655	0.84[EUR][1000 genomes]
rs13415771	0.84[EUR][1000 genomes]
rs13419072	0.84[EUR][1000 genomes]
rs1446499	0.98[ASN][1000 genomes]
rs1446500	0.98[ASN][1000 genomes]
rs17035859	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17035867	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17035884	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17035887	0.92[ASN][1000 genomes]
rs2084192	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289927	0.98[ASN][1000 genomes]
rs2289928	0.98[ASN][1000 genomes]
rs2347259	0.86[ASN][1000 genomes]
rs28516550	0.92[ASN][1000 genomes]
rs3087857	0.98[ASN][1000 genomes]
rs34581142	0.98[ASN][1000 genomes]
rs35433380	0.98[ASN][1000 genomes]
rs55872217	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56213467	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58589709	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60194846	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61132855	0.87[ASN][1000 genomes]
rs62136788	0.84[EUR][1000 genomes]
rs62136818	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62136819	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62136820	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62136822	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62136823	0.98[ASN][1000 genomes]
rs62136825	0.98[ASN][1000 genomes]
rs62136827	0.98[ASN][1000 genomes]
rs62140550	0.98[ASN][1000 genomes]
rs62140553	0.82[ASN][1000 genomes]
rs6544939	1.00[ASN][1000 genomes]
rs6706031	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6715391	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6715620	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6716381	0.98[ASN][1000 genomes]
rs6722440	0.98[ASN][1000 genomes]
rs6729120	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6729604	0.98[ASN][1000 genomes]
rs6733548	0.98[ASN][1000 genomes]
rs6743966	0.92[ASN][1000 genomes]
rs6743994	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6745578	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6755303	0.96[ASN][1000 genomes]
rs6758093	0.98[ASN][1000 genomes]
rs6758512	0.98[ASN][1000 genomes]
rs71423929	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs720827	0.84[EUR][1000 genomes]
rs7340475	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73926966	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754411	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7565420	0.92[ASN][1000 genomes]
rs7574514	0.83[ASN][1000 genomes]
rs7574833	0.84[ASN][1000 genomes]
rs7575172	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7586004	0.92[ASN][1000 genomes]
rs7596198	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7601491	0.98[ASN][1000 genomes]
rs8861	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9973504	0.89[ASN][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	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47140600-47144400	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr2:47141400-47144200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr2:47141600-47143800	Active TSS	Aorta	Aorta
4	chr2:47141600-47144000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:47141600-47144000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:47141600-47144000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:47141600-47144000	Active TSS	Left Ventricle	heart
8	chr2:47141600-47144200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:47141600-47144200	Active TSS	Pancreas	Pancrea
10	chr2:47141600-47144400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:47141600-47144400	Active TSS	Psoas Muscle	Psoas
12	chr2:47141800-47143400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:47141800-47143800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:47141800-47144200	Active TSS	H1 Cell Line	embryonic stem cell
15	chr2:47141800-47144200	Active TSS	H9 Cell Line	embryonic stem cell
16	chr2:47141800-47144200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr2:47141800-47144200	Active TSS	Ovary	ovary
18	chr2:47142000-47143400	Active TSS	NHEK	skin
19	chr2:47142000-47143600	Active TSS	NH-A	brain
20	chr2:47142000-47143800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:47142000-47143800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:47142000-47143800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:47142000-47143800	Active TSS	Esophagus	oesophagus
24	chr2:47142000-47143800	Active TSS	Fetal Muscle Trunk	muscle
25	chr2:47142000-47143800	Active TSS	Lung	lung
26	chr2:47142000-47144000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:47142000-47144000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr2:47142000-47144000	Active TSS	Fetal Intestine Small	intestine
29	chr2:47142000-47144000	Active TSS	GM12878-XiMat	blood
30	chr2:47142000-47144000	Active TSS	K562	blood
31	chr2:47142000-47144000	Active TSS	NHDF-Ad	bronchial
32	chr2:47142000-47144200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr2:47142000-47144200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:47142000-47144200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:47142000-47144200	Active TSS	Fetal Kidney	kidney
36	chr2:47142000-47144200	Active TSS	HSMM	muscle
37	chr2:47142000-47144400	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr2:47142000-47144600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:47142200-47143200	Active TSS	Thymus	Thymus
40	chr2:47142200-47143200	Active TSS	HMEC	breast
41	chr2:47142200-47143600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:47142200-47143600	Active TSS	Placenta Amnion	Placenta Amnion
43	chr2:47142200-47143800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:47142200-47143800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:47142200-47143800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr2:47142200-47143800	Active TSS	Fetal Heart	heart
47	chr2:47142200-47143800	Active TSS	Stomach Mucosa	stomach
48	chr2:47142200-47143800	Bivalent/Poised TSS	HepG2	liver
49	chr2:47142200-47144000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:47142200-47144000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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