Variant report

Variant	rs17854665
Chromosome Location	chr7:99050039-99050040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99049934-99050452	K562	blood:	n/a	n/a
2	POLR2A	chr7:99049324-99050063	K562	blood:	n/a	n/a
3	POLR2A	chr7:99049346-99050131	HepG2	liver:	n/a	n/a
4	POLR2A	chr7:99049988-99050153	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:99049971-99050133	MCF-7	breast:	n/a	n/a
6	POLR2A	chr7:99049221-99051265	K562	blood:	n/a	n/a
7	POLR2A	chr7:99049222-99050813	K562	blood:	n/a	n/a
8	POLR2A	chr7:99049243-99050096	HL-60	blood:	n/a	n/a
9	POLR2A	chr7:99049932-99050108	GM12878	blood:	n/a	n/a
10	POLR2A	chr7:99049342-99052239	SK-N-MC	brain:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99034720..99038160-chr7:99048984..99054018,5	MCF-7	breast:
2	chr7:99049487..99052484-chr7:99154940..99156543,2	K562	blood:
3	chr7:99048592..99050764-chr7:99052793..99054929,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC073063.1-1	chr7:99049991-99050887	NONHSAT122240

No data

Variant related genes	Relation type
CPSF4	TF binding region
ENSG00000197343	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000221909	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000272647	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10251282	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10279308	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1045012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11734	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11972210	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs11978089	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17161700	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17161726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2003499	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2293256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MKK][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2404487	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2404488	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28365067	0.82[ASN][1000 genomes]
rs28377312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28460612	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28558950	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28668326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28753399	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34943973	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3528	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3823813	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41258334	0.82[ASN][1000 genomes]
rs41385645	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs45441991	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45448997	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45451992	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45461000	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45492501	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45529541	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45555335	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45592335	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55927283	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55942267	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56167514	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57367781	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57832867	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59240302	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59574285	0.82[ASN][1000 genomes]
rs59672032	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6955490	1.00[JPT][hapmap]
rs6956305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs6974831	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6976017	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[ASN][1000 genomes]
rs6977165	0.82[ASN][1000 genomes]
rs73397447	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73397481	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73397499	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73401507	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73401510	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73401516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73403247	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73403272	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73403286	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73403290	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73405247	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73711280	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73711293	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73711294	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73713507	0.88[ASN][1000 genomes]
rs73713531	0.82[ASN][1000 genomes]
rs73713580	0.82[ASN][1000 genomes]
rs7794068	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7795644	0.82[MEX][hapmap]
rs7805661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs917152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs952319	1.00[JPT][hapmap];0.83[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv888767	chr7:99017832-99050039	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv888768	chr7:99017832-99052428	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99038000-99054600	Weak transcription	Stomach Mucosa	stomach
2	chr7:99038000-99061600	Strong transcription	Fetal Stomach	stomach
3	chr7:99038200-99056200	Weak transcription	Fetal Heart	heart
4	chr7:99038200-99061800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr7:99038200-99061800	Strong transcription	Fetal Intestine Small	intestine
6	chr7:99038200-99062000	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr7:99038200-99062000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr7:99038200-99062400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:99038400-99062400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr7:99038600-99058000	Strong transcription	NHEK	skin
11	chr7:99038600-99058600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr7:99038600-99062400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr7:99038800-99058000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr7:99039000-99055000	Strong transcription	Placenta	Placenta
15	chr7:99039000-99059000	Strong transcription	Fetal Intestine Large	intestine
16	chr7:99039200-99054000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr7:99039200-99058000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr7:99039200-99058000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr7:99039200-99058200	Strong transcription	Dnd41	blood
20	chr7:99039200-99061600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:99039400-99059600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:99039600-99058000	Strong transcription	HMEC	breast
23	chr7:99039600-99062000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr7:99039800-99054400	Weak transcription	Right Atrium	heart
25	chr7:99040000-99058400	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:99040000-99058600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:99040000-99059000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr7:99040000-99060600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr7:99040200-99058200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr7:99040200-99059400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:99040200-99059400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr7:99040400-99058200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr7:99040400-99058400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:99040400-99058400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr7:99040400-99058600	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr7:99040400-99058600	Strong transcription	Fetal Lung	lung
37	chr7:99040400-99059000	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr7:99040400-99059600	Strong transcription	Primary T cells from cord blood	blood
39	chr7:99040400-99060800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr7:99040400-99062000	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr7:99040600-99057200	Strong transcription	Ovary	ovary
42	chr7:99040600-99058400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr7:99040800-99055000	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr7:99040800-99062000	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr7:99041000-99053000	Strong transcription	HSMMtube	muscle
46	chr7:99041000-99057600	Strong transcription	Fetal Brain Female	brain
47	chr7:99041000-99058400	Strong transcription	Liver	Liver
48	chr7:99041000-99058600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr7:99041000-99058600	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr7:99041200-99058600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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