Variant report

Variant	rs6716978
Chromosome Location	chr2:53997624-53997625
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	STAT3	chr2:53997424-53997689	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFF	chr2:53997376-53997753	K562	blood:	n/a	n/a
3	BACH1	chr2:53997428-53997751	K562	blood:	n/a	chr2:53997554-53997568
4	FOS	chr2:53997327-53997801	MCF10A-Er-Src	breast:	n/a	chr2:53997557-53997565 chr2:53997557-53997565 chr2:53997557-53997564
5	ZNF384	chr2:53996974-53997990	K562	blood:	n/a	n/a
6	FOS	chr2:53997376-53997698	MCF10A-Er-Src	breast:	n/a	chr2:53997557-53997565 chr2:53997557-53997565 chr2:53997557-53997564
7	TEAD4	chr2:53997323-53997736	K562	blood:	n/a	n/a
8	TBL1XR1	chr2:53997254-53997634	K562	blood:	n/a	n/a
9	POLR2A	chr2:53993983-53998651	GM12878	blood:	n/a	n/a
10	IRF1	chr2:53997166-53997748	K562	blood:	n/a	chr2:53997556-53997565 chr2:53997200-53997210 chr2:53997458-53997478
11	GATA1	chr2:53997167-53997806	PBDE	blood:	n/a	n/a
12	MAFK	chr2:53997411-53997680	HepG2	liver:	n/a	chr2:53997558-53997567 chr2:53997557-53997567
13	MAFK	chr2:53997354-53997733	K562	blood:	n/a	chr2:53997558-53997567 chr2:53997557-53997567
14	FOS	chr2:53997334-53997726	MCF10A-Er-Src	breast:	n/a	chr2:53997557-53997565 chr2:53997557-53997565 chr2:53997557-53997564
15	POLR2A	chr2:53994075-53999332	K562	blood:	n/a	n/a
16	STAT3	chr2:53997296-53997742	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr2:53996232-53997835	K562	blood:	n/a	chr2:53997335-53997342 chr2:53997481-53997488 chr2:53997557-53997566 chr2:53997461-53997470
18	JUND	chr2:53997423-53997712	K562	blood:	n/a	chr2:53997557-53997565 chr2:53997557-53997565 chr2:53997557-53997564
19	POLR2A	chr2:53996150-53998649	Hela-S3	cervix:	n/a	n/a
20	TAL1	chr2:53997255-53997649	K562	blood:	n/a	n/a
21	POLR2A	chr2:53997144-53998202	MCF10A-Er-Src	breast:	n/a	n/a
22	E2F4	chr2:53997334-53997690	MCF10A-Er-Src	breast:	n/a	n/a
23	RCOR1	chr2:53997400-53997856	K562	blood:	n/a	n/a
24	FOS	chr2:53997384-53997738	MCF10A-Er-Src	breast:	n/a	chr2:53997557-53997565 chr2:53997557-53997565 chr2:53997557-53997564
25	ARID3A	chr2:53997093-53997781	K562	blood:	n/a	n/a
26	MYC	chr2:53997125-53998195	MCF10A-Er-Src	breast:	n/a	chr2:53997557-53997566

No.	Distal block	Cell Line	Cell type
1	chr2:53996518..54000180-chr2:54012874..54016675,4	K562	blood:
2	chr2:53993244..53996304-chr2:53997102..54000368,4	MCF-7	breast:
3	chr2:53993518..53997677-chr2:54010995..54015634,7	MCF-7	breast:

Variant related genes	Relation type
GPR75-ASB3	TF binding region
ENSG00000068912	Chromatin interaction
ENSG00000143942	Chromatin interaction
ENSG00000115239	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10180492	1.00[JPT][hapmap]
rs10205469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10208649	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1049894	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11890472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13387291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13401719	1.00[CHB][hapmap]
rs13408425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13417051	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17045242	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6545369	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6731217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6751340	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6756424	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53995400-54003600	Weak transcription	Small Intestine	intestine
2	chr2:53995600-54005800	Weak transcription	HSMM	muscle
3	chr2:53995600-54007400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:53995600-54007400	Weak transcription	Fetal Muscle Leg	muscle
5	chr2:53995600-54007800	Weak transcription	Placenta	Placenta
6	chr2:53995600-54008400	Weak transcription	Ovary	ovary
7	chr2:53995600-54009000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:53995600-54009000	Weak transcription	Lung	lung
9	chr2:53995600-54011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:53995600-54011400	Weak transcription	Right Atrium	heart
11	chr2:53995600-54011600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:53995600-54012000	Weak transcription	Left Ventricle	heart
13	chr2:53995600-54012800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:53995800-53999600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:53995800-54000600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr2:53995800-54000600	Weak transcription	Fetal Intestine Small	intestine
17	chr2:53995800-54001000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr2:53995800-54001200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:53995800-54003000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:53995800-54006800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr2:53995800-54008600	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:53995800-54011400	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:53995800-54011600	Weak transcription	Psoas Muscle	Psoas
24	chr2:53995800-54011800	Weak transcription	Right Ventricle	heart
25	chr2:53995800-54012000	Weak transcription	Adipose Nuclei	Adipose
26	chr2:53995800-54012200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:53995800-54012400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr2:53995800-54012600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr2:53996000-53998400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:53996000-54000800	Weak transcription	Fetal Intestine Large	intestine
31	chr2:53996000-54001200	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:53996000-54004400	Weak transcription	Osteobl	bone
33	chr2:53996000-54005800	Weak transcription	Liver	Liver
34	chr2:53996000-54006800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr2:53996000-54009000	Weak transcription	Brain Substantia Nigra	brain
36	chr2:53996000-54011000	Weak transcription	Fetal Brain Male	brain
37	chr2:53996000-54011200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:53996000-54011600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:53996000-54011600	Weak transcription	Fetal Lung	lung
40	chr2:53996000-54011800	Weak transcription	NHDF-Ad	bronchial
41	chr2:53996200-53998200	Enhancers	HepG2	liver
42	chr2:53996200-53999200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:53996200-54000600	Weak transcription	Fetal Stomach	stomach
44	chr2:53996200-54003000	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:53996200-54003600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr2:53996200-54004400	Weak transcription	Primary B cells from cord blood	blood
47	chr2:53996200-54006400	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr2:53996200-54006800	Weak transcription	NH-A	brain
49	chr2:53996200-54007200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:53996200-54009800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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