Variant report

Variant	rs2075672
Chromosome Location	chr7:100240296-100240297
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	MAZ	chr7:100240291-100240598	HepG2	liver:	n/a	chr7:100240488-100240498
2	POLR2A	chr7:100239232-100240415	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr7:100240095-100240479	HepG2	liver:	n/a	n/a
4	PAX5	chr7:100240197-100240472	GM12878	blood:	n/a	n/a
5	TAF1	chr7:100239900-100240464	K562	blood:	n/a	n/a
6	RAD21	chr7:100239864-100240328	H1-hESC	embryonic stem cell:	n/a	chr7:100240086-100240096 chr7:100240086-100240098
7	POLR2A	chr7:100239912-100240494	K562	blood:	n/a	n/a
8	MYC	chr7:100238990-100240373	K562	blood:	n/a	chr7:100239810-100239820 chr7:100239811-100239821 chr7:100239810-100239825 chr7:100240083-100240093 chr7:100239730-100239746 chr7:100239370-100239379
9	BHLHE40	chr7:100240061-100240404	K562	blood:	n/a	n/a
10	POLR2A	chr7:100240080-100240516	HepG2	liver:	n/a	n/a
11	TBL1XR1	chr7:100240175-100240355	K562	blood:	n/a	n/a
12	HMGN3	chr7:100240208-100240510	K562	blood:	n/a	n/a
13	TBP	chr7:100240075-100240514	K562	blood:	n/a	n/a
14	MYC	chr7:100238260-100240511	K562	blood:	n/a	chr7:100240488-100240498 chr7:100238963-100238972 chr7:100239810-100239820 chr7:100239811-100239821 chr7:100239810-100239825 chr7:100240083-100240093 chr7:100239730-100239746 chr7:100239370-100239379
15	PML	chr7:100240063-100240455	K562	blood:	n/a	n/a
16	ELF1	chr7:100240079-100240419	K562	blood:	n/a	n/a
17	POLR2A	chr7:100240044-100240500	HepG2	liver:	n/a	n/a
18	UBTF	chr7:100239966-100240358	K562	blood:	n/a	n/a
19	POLR2A	chr7:100240149-100240540	HepG2	liver:	n/a	n/a
20	RCOR1	chr7:100240086-100240391	K562	blood:	n/a	n/a
21	EBF1	chr7:100240001-100240581	GM12878	blood:	n/a	chr7:100240347-100240358 chr7:100240181-100240191 chr7:100240180-100240193 chr7:100240182-100240191
22	MAX	chr7:100239635-100240493	K562	blood:	n/a	chr7:100239810-100239820 chr7:100239811-100239821 chr7:100239810-100239825 chr7:100240083-100240093 chr7:100239730-100239746
23	CEBPD	chr7:100238432-100240610	K562	blood:	n/a	n/a
24	EGR1	chr7:100240277-100240614	K562	blood:	n/a	n/a
25	POLR2A	chr7:100238085-100240520	K562	blood:	n/a	n/a
26	MAX	chr7:100238962-100240694	HepG2	liver:	n/a	chr7:100240488-100240498 chr7:100238963-100238972 chr7:100239810-100239820 chr7:100239811-100239821 chr7:100239810-100239825 chr7:100240083-100240093 chr7:100239730-100239746 chr7:100239370-100239379
27	MYC	chr7:100238149-100240497	K562	blood:	n/a	chr7:100238963-100238972 chr7:100239810-100239820 chr7:100239811-100239821 chr7:100239810-100239825 chr7:100240083-100240093 chr7:100239730-100239746 chr7:100239370-100239379
28	ZEB1	chr7:100240079-100240410	GM12878	blood:	n/a	n/a
29	POLR2A	chr7:100240230-100240408	HepG2	liver:	n/a	n/a
30	CHD2	chr7:100240172-100240307	K562	blood:	n/a	n/a
31	HDAC2	chr7:100240209-100240474	K562	blood:	n/a	n/a
32	HEY1	chr7:100240046-100240602	HepG2	liver:	n/a	n/a
33	IRF1	chr7:100239931-100240619	K562	blood:	n/a	chr7:100240251-100240265 chr7:100240165-100240178 chr7:100240164-100240178 chr7:100240165-100240178 chr7:100240164-100240184 chr7:100240166-100240176 chr7:100240162-100240179 chr7:100240162-100240176
34	POLR2A	chr7:100238886-100240793	HepG2	liver:	n/a	n/a
35	POLR2A	chr7:100239540-100240521	K562	blood:	n/a	n/a
36	RCOR1	chr7:100240019-100240369	K562	blood:	n/a	n/a
37	CTCF	chr7:100239805-100240393	K562	blood:	n/a	chr7:100240081-100240097
38	EGR1	chr7:100240203-100240676	K562	blood:	n/a	n/a
39	ZBTB7A	chr7:100238286-100240829	K562	blood:	n/a	chr7:100240088-100240097
40	IRF1	chr7:100238658-100240441	K562	blood:	n/a	chr7:100240251-100240265 chr7:100240165-100240178 chr7:100240164-100240178 chr7:100240165-100240178 chr7:100240164-100240184 chr7:100240166-100240176 chr7:100240162-100240179 chr7:100240162-100240176
41	ZBTB7A	chr7:100237688-100240722	K562	blood:	n/a	chr7:100240088-100240097
42	MAX	chr7:100240145-100240497	K562	blood:	n/a	n/a
43	EBF1	chr7:100239993-100240533	GM12878	blood:	n/a	chr7:100240347-100240358 chr7:100240181-100240191 chr7:100240180-100240193 chr7:100240182-100240191
44	POLR2A	chr7:100237685-100240723	K562	blood:	n/a	n/a
45	ZNF143	chr7:100239951-100240443	K562	blood:	n/a	chr7:100240089-100240099
46	NR2F2	chr7:100237709-100240776	K562	blood:	n/a	n/a
47	MYC	chr7:100238988-100240523	K562	blood:	n/a	chr7:100240488-100240498 chr7:100239810-100239820 chr7:100239811-100239821 chr7:100239810-100239825 chr7:100240083-100240093 chr7:100239730-100239746 chr7:100239370-100239379
48	GABPA	chr7:100239566-100240564	K562	blood:	n/a	n/a
49	POLR2A	chr7:100238962-100240487	K562	blood:	n/a	n/a
50	POLR2A	chr7:100240037-100240557	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:100231005..100233998-chr7:100238319..100240300,2	MCF-7	breast:
2	chr7:100207856..100214217-chr7:100235772..100240956,9	K562	blood:
3	chr7:100176059..100178977-chr7:100238614..100240388,2	K562	blood:
4	chr7:100238260..100241603-chr7:100301224..100306213,4	K562	blood:
5	chr7:100235870..100241765-chr7:100269603..100274523,10	K562	blood:
6	chr7:100208330..100211092-chr7:100239329..100241095,2	MCF-7	breast:
7	chr7:100207856..100215304-chr7:100235701..100242038,10	K562	blood:
8	chr7:100182236..100184425-chr7:100238898..100241261,2	MCF-7	breast:
9	chr7:100223053..100226003-chr7:100238727..100241235,2	MCF-7	breast:
10	chr7:100024854..100029212-chr7:100238393..100241596,5	K562	blood:
11	chr7:100025315..100028678-chr7:100237515..100241293,6	K562	blood:
12	chr7:100223071..100228603-chr7:100236890..100242224,6	K562	blood:
13	chr7:100200627..100204986-chr7:100237375..100241909,8	K562	blood:
14	chr7:100238702..100243589-chr7:100269441..100273725,6	MCF-7	breast:
15	chr7:100234354..100241214-chr7:100269812..100274154,10	K562	blood:
16	chr7:100229346..100236063-chr7:100236439..100240927,7	K562	blood:
17	chr7:100166949..100169770-chr7:100238447..100240674,2	K562	blood:
18	chr7:100238851..100242571-chr7:100242728..100246485,5	K562	blood:
19	chr7:100183091..100184798-chr7:100238306..100241212,2	K562	blood:
20	chr7:99933746..99935432-chr7:100238068..100240501,2	K562	blood:
21	chr7:100183091..100185790-chr7:100237185..100241212,3	K562	blood:
22	chr7:100200263..100204018-chr7:100237004..100241425,9	K562	blood:

Variant related genes	Relation type
TFR2	TF binding region
ENSG00000077080	Chromatin interaction
ENSG00000242294	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000184414	Chromatin interaction
ENSG00000272752	Chromatin interaction
ENSG00000106330	Chromatin interaction
ENSG00000106336	Chromatin interaction
ENSG00000172354	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000106327	Chromatin interaction
ENSG00000172336	Chromatin interaction
ENSG00000224729	Chromatin interaction
ENSG00000106333	Chromatin interaction
ENSG00000077454	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10277087	0.82[MEX][hapmap]
rs10487157	0.86[JPT][hapmap]
rs11764045	0.86[JPT][hapmap]
rs12532878	0.86[JPT][hapmap]
rs1617640	0.86[MEX][hapmap]
rs1734908	0.86[MEX][hapmap]
rs1734910	0.86[MEX][hapmap]
rs2075674	0.84[JPT][hapmap]
rs221801	0.82[MEX][hapmap]
rs2231170	0.86[JPT][hapmap]
rs2231172	0.86[JPT][hapmap]
rs4548095	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4729597	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4729601	0.86[JPT][hapmap]
rs504141	0.82[MEX][hapmap]
rs507392	0.86[MEX][hapmap]
rs551238	0.86[MEX][hapmap]
rs62482241	0.91[ASN][1000 genomes]
rs6969584	0.86[JPT][hapmap]
rs6969697	0.86[JPT][hapmap]
rs7385804	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7786877	0.85[JPT][hapmap]
rs7812123	0.86[JPT][hapmap]
rs7812235	0.86[JPT][hapmap]
rs9801017	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829095	chr7:99814675-100494084	Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	393 gene(s)	inside rSNPs	diseases
2	nsv888779	chr7:100014711-100313420	Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	321 gene(s)	inside rSNPs	diseases
3	nsv888785	chr7:100141861-100313420	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv888786	chr7:100159567-100313420	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv831072	chr7:100162503-100362835	Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv888791	chr7:100221867-100371114	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv607933	chr7:100240191-100365613	Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
8	nsv470381	chr7:100240191-100431980	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Red blood cell traits	23222517	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2075672	SERPINE1	cis	cerebellum	SCAN
rs2075672	MOSPD3	cis	Whole Blood	GTEx
rs2075672	TAC1	cis	parietal	SCAN
rs2075672	POLR2J	cis	parietal	SCAN
rs2075672	DLX5	cis	cerebellum	SCAN
rs2075672	TSC22D4	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:100231400-100242400	Weak transcription	Right Atrium	heart
2	chr7:100231400-100247200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:100237600-100241200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:100237800-100240800	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr7:100238000-100241400	Enhancers	H1 Cell Line	embryonic stem cell
6	chr7:100238400-100240400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
7	chr7:100238400-100252600	Weak transcription	Gastric	stomach
8	chr7:100238600-100244600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:100238800-100240400	Active TSS	Liver	Liver
10	chr7:100238800-100240600	Weak transcription	Fetal Brain Female	brain
11	chr7:100238800-100241000	Enhancers	Primary hematopoietic stem cells	blood
12	chr7:100239000-100240600	Enhancers	Stomach Mucosa	stomach
13	chr7:100239200-100241000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr7:100239400-100241400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:100239600-100240400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr7:100239600-100240600	Flanking Active TSS	K562	blood
17	chr7:100239800-100240400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr7:100239800-100240600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr7:100239800-100240800	Enhancers	Primary B cells from peripheral blood	blood
20	chr7:100239800-100240800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr7:100240000-100240400	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr7:100240000-100240600	Bivalent Enhancer	Placenta	Placenta
23	chr7:100240000-100240600	Enhancers	GM12878-XiMat	blood
24	chr7:100240000-100240800	Weak transcription	Pancreas	Pancrea
25	chr7:100240200-100240400	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr7:100240200-100240400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr7:100240200-100240400	Enhancers	Spleen	Spleen
28	chr7:100240200-100240400	Active TSS	HepG2	liver
29	chr7:100240200-100240800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:100240200-100241400	Enhancers	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links