Variant report

Variant	rs2231656
Chromosome Location	chr9:100935221-100935222
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr9:100935100-100935250	SAEC	small airway:	n/a	n/a
2	ZNF263	chr9:100934864-100936123	HEK293-T-REx	kidney:	n/a	n/a
3	KAP1	chr9:100934880-100935461	HEK293	kidney:	n/a	n/a
4	SMC3	chr9:100934947-100935225	Hela-S3	cervix:	n/a	n/a
5	MYC	chr9:100935212-100935238	MCF-7	breast:	n/a	n/a
6	NR2F2	chr9:100934768-100935558	MCF-7	breast:	n/a	n/a
7	NR3C1	chr9:100934916-100935247	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr9:100935172-100935254	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr9:100934804-100935574	MCF-7	breast:	n/a	n/a
10	SIN3A	chr9:100935149-100935349	H1-hESC	embryonic stem cell:	n/a	n/a
11	MAX	chr9:100934738-100935564	MCF-7	breast:	n/a	n/a
12	GATA3	chr9:100934964-100935419	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr9:100934686-100935745	MCF-7	breast:	n/a	n/a
14	ELF1	chr9:100934762-100935475	MCF-7	breast:	n/a	n/a
15	NR2F2	chr9:100934778-100935458	MCF-7	breast:	n/a	n/a
16	ZNF217	chr9:100934879-100935413	MCF-7	breast:	n/a	n/a
17	NFIC	chr9:100934772-100935409	ECC-1	luminal epithelium:	n/a	n/a
18	MYC	chr9:100934968-100935347	MCF-7	breast:	n/a	n/a
19	TCF7L2	chr9:100934952-100935398	MCF-7	breast:	n/a	n/a
20	FOXM1	chr9:100934779-100935377	ECC-1	luminal epithelium:	n/a	n/a
21	RAD21	chr9:100934951-100935226	Hela-S3	cervix:	n/a	n/a
22	TCF12	chr9:100934793-100935517	ECC-1	luminal epithelium:	n/a	chr9:100934976-100934983
23	HDAC2	chr9:100934862-100935240	HepG2	liver:	n/a	n/a
24	ESR1	chr9:100934877-100935299	ECC-1	luminal epithelium:	n/a	n/a
25	GATA3	chr9:100934827-100935519	MCF-7	breast:	n/a	n/a
26	TCF7L2	chr9:100935015-100935285	PANC-1	pancreas:	n/a	n/a
27	MAX	chr9:100934933-100935462	ECC-1	luminal epithelium:	n/a	n/a
28	TCF12	chr9:100934809-100935613	ECC-1	luminal epithelium:	n/a	chr9:100934976-100934983
29	TFAP2C	chr9:100934855-100935297	Hela-S3	cervix:	n/a	n/a
30	EP300	chr9:100934770-100935338	MCF-7	breast:	n/a	n/a
31	EP300	chr9:100934785-100935312	ECC-1	luminal epithelium:	n/a	n/a
32	HDAC2	chr9:100934818-100935535	MCF-7	breast:	n/a	n/a
33	NFIC	chr9:100934739-100935385	ECC-1	luminal epithelium:	n/a	n/a
34	FOXA1	chr9:100934854-100935285	ECC-1	luminal epithelium:	n/a	n/a
35	KAP1	chr9:100934918-100935483	U2OS	brain:	n/a	n/a
36	RAD21	chr9:100934825-100935378	MCF-7	breast:	n/a	n/a
37	YY1	chr9:100934905-100935409	ECC-1	luminal epithelium:	n/a	n/a
38	EP300	chr9:100934765-100935503	ECC-1	luminal epithelium:	n/a	n/a
39	ESR1	chr9:100934809-100935387	ECC-1	luminal epithelium:	n/a	n/a
40	HDAC2	chr9:100934740-100935442	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:100932527..100936703-chr9:100952110..100957364,6	MCF-7	breast:
2	chr9:100934229..100937131-chr9:101015572..101018332,2	MCF-7	breast:
3	chr9:100934419..100936711-chr9:100950978..100955014,5	MCF-7	breast:
4	chr9:100934290..100936965-chr9:101016512..101018556,3	K562	blood:

No data

Variant related genes	Relation type
CORO2A	TF binding region
ENSG00000106789	Chromatin interaction
ENSG00000095383	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10491724	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12551204	0.86[CHB][hapmap];0.90[ASN][1000 genomes]
rs12552786	0.80[CHD][hapmap]
rs16913411	0.82[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16913573	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs1983815	0.92[CHB][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2231652	0.92[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs2275710	0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs3758263	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56735263	0.83[ASN][1000 genomes]
rs57830760	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7040921	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482635	chr9:100775549-100953239	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv893613	chr9:100885779-100943397	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100920400-100942200	Weak transcription	Primary T cells from cord blood	blood
2	chr9:100924600-100939000	Enhancers	Duodenum Mucosa	Duodenum
3	chr9:100927000-100936800	Weak transcription	Thymus	Thymus
4	chr9:100929800-100935800	Enhancers	K562	blood
5	chr9:100930800-100936000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:100930800-100938000	Genic enhancers	Fetal Intestine Small	intestine
7	chr9:100931400-100937400	Weak transcription	Spleen	Spleen
8	chr9:100931800-100954400	Weak transcription	Right Atrium	heart
9	chr9:100932000-100937400	Weak transcription	Primary B cells from cord blood	blood
10	chr9:100932000-100937400	Enhancers	HepG2	liver
11	chr9:100932200-100937600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:100932400-100937400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:100932400-100937600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr9:100932600-100937200	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr9:100932800-100936200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:100932800-100951200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:100933000-100936400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr9:100933200-100935600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr9:100933400-100935400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:100933400-100935400	Enhancers	Fetal Thymus	thymus
21	chr9:100933400-100935600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr9:100933400-100935800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr9:100933400-100936000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:100933400-100951400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr9:100933600-100935400	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr9:100933600-100935600	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr9:100933600-100935800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr9:100933600-100936000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr9:100933600-100942600	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr9:100933800-100937600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr9:100933800-100942400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:100933800-100950200	Weak transcription	Colonic Mucosa	Colon
33	chr9:100933800-100951400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:100934000-100935400	Enhancers	NHEK	skin
35	chr9:100934400-100936000	Enhancers	Stomach Mucosa	stomach
36	chr9:100934400-100954000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr9:100934600-100937000	Enhancers	Small Intestine	intestine
38	chr9:100934800-100935400	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr9:100934800-100935600	Enhancers	Hela-S3	cervix
40	chr9:100934800-100936000	Enhancers	Liver	Liver
41	chr9:100935000-100935400	Enhancers	H9 Cell Line	embryonic stem cell
42	chr9:100935000-100935400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr9:100935000-100935400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr9:100935000-100935600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:100935000-100935600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:100935000-100935600	Enhancers	Esophagus	oesophagus
47	chr9:100935000-100935600	Enhancers	HSMMtube	muscle
48	chr9:100935000-100935800	Genic enhancers	Fetal Intestine Large	intestine
49	chr9:100935000-100936600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:100935200-100935400	Enhancers	Gastric	stomach

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