Variant report

Variant	rs6748685
Chromosome Location	chr2:38826925-38826926
allele	C/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	MYBL2	chr2:38825986-38827459	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:38825324-38828171	HepG2	liver:	n/a	n/a
3	CEBPB	chr2:38826899-38827295	HepG2	liver:	n/a	chr2:38827101-38827114 chr2:38827101-38827112 chr2:38827131-38827143
4	FOXA1	chr2:38826773-38827151	HepG2	liver:	n/a	n/a
5	FOXA2	chr2:38826788-38827234	HepG2	liver:	n/a	n/a
6	TCF7L2	chr2:38826736-38827169	HEK293	kidney:	n/a	chr2:38826967-38826977 chr2:38826970-38826977
7	TBL1XR1	chr2:38826587-38828368	K562	blood:	n/a	n/a
8	TEAD4	chr2:38826023-38827980	HepG2	liver:	n/a	n/a
9	EP300	chr2:38826695-38827353	HepG2	liver:	n/a	chr2:38826791-38826805
10	TCF7L2	chr2:38826803-38827095	PANC-1	pancreas:	n/a	chr2:38826967-38826977 chr2:38826970-38826977
11	EP300	chr2:38826908-38827259	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:38826818-38827590	MCF10A-Er-Src	breast:	n/a	n/a
13	MBD4	chr2:38826718-38827616	HepG2	liver:	n/a	n/a
14	FOXA1	chr2:38826837-38827242	HepG2	liver:	n/a	n/a
15	HDAC2	chr2:38826798-38827276	HepG2	liver:	n/a	n/a
16	HEY1	chr2:38826591-38827291	HepG2	liver:	n/a	n/a
17	HDAC2	chr2:38826741-38827366	HepG2	liver:	n/a	n/a
18	SP1	chr2:38826730-38827255	HepG2	liver:	n/a	n/a
19	TEAD4	chr2:38826847-38828457	K562	blood:	n/a	n/a
20	MAFK	chr2:38826849-38827148	HepG2	liver:	n/a	n/a
21	HEY1	chr2:38826792-38827257	HepG2	liver:	n/a	n/a
22	POLR2A	chr2:38821640-38832164	K562	blood:	n/a	n/a
23	MYBL2	chr2:38826556-38828048	HepG2	liver:	n/a	n/a
24	NFIC	chr2:38825976-38827458	HepG2	liver:	n/a	chr2:38826326-38826342 chr2:38826316-38826344
25	MBD4	chr2:38826651-38828360	HepG2	liver:	n/a	n/a
26	HNF4G	chr2:38826823-38827234	HepG2	liver:	n/a	n/a
27	FOXA2	chr2:38826545-38827356	HepG2	liver:	n/a	n/a
28	TBP	chr2:38826845-38827321	HepG2	liver:	n/a	n/a
29	POLR2A	chr2:38826352-38827348	HepG2	liver:	n/a	n/a
30	RXRA	chr2:38826859-38827198	HepG2	liver:	n/a	n/a
31	EP300	chr2:38826736-38827191	HepG2	liver:	n/a	chr2:38826791-38826805
32	FOXA1	chr2:38826708-38827346	HepG2	liver:	n/a	n/a
33	MAFK	chr2:38826828-38827162	HepG2	liver:	n/a	n/a
34	TCF7L2	chr2:38826652-38827295	HepG2	liver:	n/a	chr2:38826967-38826977 chr2:38826970-38826977
35	NFIC	chr2:38826707-38827326	HepG2	liver:	n/a	n/a
36	FOXA1	chr2:38826716-38827433	HepG2	liver:	n/a	chr2:38827379-38827391
37	HNF4A	chr2:38826898-38827156	HepG2	liver:	n/a	n/a
38	MAFF	chr2:38826850-38827150	HepG2	liver:	n/a	n/a
39	POLR2A	chr2:38825282-38829280	K562	blood:	n/a	n/a
40	IRF1	chr2:38826885-38827238	K562	blood:	n/a	n/a
41	ARID3A	chr2:38826716-38827468	HepG2	liver:	n/a	n/a
42	CEBPB	chr2:38826873-38827210	HepG2	liver:	n/a	chr2:38827101-38827114 chr2:38827101-38827112 chr2:38827131-38827143

No.	Distal block	Cell Line	Cell type
1	chr2:38823060..38827854-chr2:38827983..38831423,11	MCF-7	breast:
2	chr2:38825670..38832919-chr2:38891527..38903424,21	K562	blood:
3	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
4	chr2:38824811..38832919-chr2:38891494..38898299,16	K562	blood:
5	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
6	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
7	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
8	chr2:38821957..38830238-chr2:38965333..38974515,17	K562	blood:
9	chr2:38816590..38821819-chr2:38825503..38830021,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235586	TF binding region
ENSG00000235586	Chromatin interaction
ENSG00000232518	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1543881	0.81[AMR][1000 genomes]
rs17603782	0.81[AMR][1000 genomes]
rs6710613	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907906	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907929	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73929052	0.81[AMR][1000 genomes]
rs7580657	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7594264	0.86[AFR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
2	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
5	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
6	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
11	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:38810000-38827600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:38813400-38827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:38818400-38827600	Weak transcription	Placenta	Placenta
15	chr2:38819600-38827400	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr2:38820200-38827800	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr2:38821000-38827000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:38821000-38827400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:38822400-38827600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr2:38822400-38828600	Weak transcription	Lung	lung
21	chr2:38822800-38830400	Active TSS	Primary T cells fromperipheralblood	blood
22	chr2:38823200-38827000	Enhancers	Colon Smooth Muscle	Colon
23	chr2:38824000-38827000	Enhancers	Fetal Lung	lung
24	chr2:38824400-38828200	Enhancers	Fetal Heart	heart
25	chr2:38824600-38827400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr2:38824600-38827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:38825000-38827200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:38825000-38827400	Enhancers	Hela-S3	cervix
29	chr2:38825000-38830600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:38825200-38827000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr2:38825200-38827000	Enhancers	Fetal Intestine Small	intestine
32	chr2:38825200-38827200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:38825200-38827400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:38825200-38827400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr2:38825200-38828400	Enhancers	Liver	Liver
36	chr2:38825200-38831000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:38825400-38827000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:38825400-38827000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:38825400-38827000	Enhancers	NH-A	brain
40	chr2:38825400-38827200	Enhancers	Brain Substantia Nigra	brain
41	chr2:38825400-38827400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr2:38825400-38827400	Enhancers	Fetal Intestine Large	intestine
43	chr2:38825400-38827600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:38825400-38828000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr2:38825400-38828000	Enhancers	Primary T cells from cord blood	blood
46	chr2:38825400-38828400	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr2:38825600-38827000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr2:38825600-38827000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr2:38825600-38827000	Enhancers	Brain Anterior Caudate	brain
50	chr2:38825600-38827000	Enhancers	HMEC	breast

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