Variant report

Variant	rs6544170
Chromosome Location	chr2:38820522-38820523
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	FOS	chr2:38819974-38820564	MCF10A-Er-Src	breast:	n/a	chr2:38820068-38820077 chr2:38820327-38820339 chr2:38820162-38820171 chr2:38820068-38820075
2	FOS	chr2:38819907-38820543	MCF10A-Er-Src	breast:	n/a	chr2:38820068-38820077 chr2:38820327-38820339 chr2:38820162-38820171 chr2:38820068-38820075
3	FOS	chr2:38820180-38820531	MCF10A-Er-Src	breast:	n/a	chr2:38820327-38820339
4	POLR2A	chr2:38819159-38821053	K562	blood:	n/a	n/a
5	STAT3	chr2:38820007-38820593	MCF10A-Er-Src	breast:	n/a	chr2:38820338-38820347 chr2:38820339-38820348 chr2:38820067-38820076
6	POLR2A	chr2:38820099-38821144	K562	blood:	n/a	n/a
7	CEBPB	chr2:38820041-38820668	A549	lung:	n/a	chr2:38820184-38820196
8	SP1	chr2:38820093-38820587	A549	lung:	n/a	n/a
9	POLR2A	chr2:38820347-38820546	K562	blood:	n/a	n/a
10	MAFK	chr2:38820201-38820544	IMR90	lung:	n/a	n/a
11	E2F4	chr2:38820183-38820700	MCF10A-Er-Src	breast:	n/a	n/a
12	FOS	chr2:38819979-38820555	MCF10A-Er-Src	breast:	n/a	chr2:38820068-38820077 chr2:38820327-38820339 chr2:38820162-38820171 chr2:38820068-38820075
13	POLR2A	chr2:38820467-38820952	K562	blood:	n/a	n/a
14	BCL3	chr2:38819993-38820617	A549	lung:	n/a	chr2:38820339-38820348 chr2:38820338-38820347 chr2:38820067-38820076
15	CEBPB	chr2:38820125-38820560	IMR90	lung:	n/a	chr2:38820184-38820196
16	STAT3	chr2:38819969-38820555	MCF10A-Er-Src	breast:	n/a	chr2:38820338-38820347 chr2:38820339-38820348 chr2:38820067-38820076
17	FOSL2	chr2:38820009-38820626	A549	lung:	n/a	chr2:38820068-38820077 chr2:38820327-38820339 chr2:38820162-38820171 chr2:38820068-38820075
18	POLR2A	chr2:38820180-38820601	HepG2	liver:	n/a	n/a
19	STAT3	chr2:38819969-38820581	MCF10A-Er-Src	breast:	n/a	chr2:38820338-38820347 chr2:38820339-38820348 chr2:38820067-38820076

No.	Distal block	Cell Line	Cell type
1	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
2	chr2:38820462..38822126-chr2:38823935..38825729,2	MCF-7	breast:
3	chr2:38819178..38822144-chr2:38914195..38916450,2	K562	blood:
4	chr2:38819202..38822030-chr2:38909046..38911240,2	K562	blood:
5	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
6	chr2:38816590..38821819-chr2:38825503..38830021,9	MCF-7	breast:
7	chr2:38764122..38766305-chr2:38818986..38821138,2	K562	blood:
8	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
9	chr2:38778255..38779937-chr2:38819083..38821616,2	K562	blood:
10	chr2:38820056..38822885-chr2:38968180..38969856,2	MCF-7	breast:

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

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10204680	0.82[MEX][hapmap]
rs10495880	0.86[CHD][hapmap];0.91[MEX][hapmap]
rs12105827	0.90[EUR][1000 genomes]
rs12995222	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs12996029	0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap]
rs1540436	0.81[JPT][hapmap]
rs17421399	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs17421503	0.86[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap]
rs17493321	0.94[CEU][hapmap];0.90[EUR][1000 genomes]
rs17493370	0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap]
rs17493538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17493573	0.81[JPT][hapmap]
rs17493594	0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17575960	0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs1864828	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3213851	0.83[ASN][1000 genomes]
rs34218951	0.90[EUR][1000 genomes]
rs34533895	0.87[ASN][1000 genomes]
rs3731843	0.81[CHD][hapmap]
rs4268910	0.86[CHD][hapmap];1.00[GIH][hapmap]
rs56217714	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6721860	0.84[EUR][1000 genomes]
rs67326552	0.82[AFR][1000 genomes]
rs6742843	0.84[MEX][hapmap]
rs6745023	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6757844	0.82[EUR][1000 genomes]
rs7573095	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7574556	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs919698	0.89[YRI][hapmap];0.83[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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
3	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
4	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
7	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
8	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:38798800-38822000	Weak transcription	NHEK	skin
12	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:38808200-38824400	Weak transcription	Hela-S3	cervix
15	chr2:38808800-38821800	Weak transcription	HMEC	breast
16	chr2:38808800-38825200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr2:38808800-38825400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
21	chr2:38809000-38824200	Weak transcription	Liver	Liver
22	chr2:38809000-38825600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr2:38809400-38825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:38810000-38827600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr2:38812600-38823800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:38813000-38821800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr2:38813000-38821800	Weak transcription	Adipose Nuclei	Adipose
29	chr2:38813000-38823800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr2:38813200-38826000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:38813400-38827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr2:38813800-38825400	Weak transcription	Primary T cells from cord blood	blood
33	chr2:38814400-38825200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr2:38814400-38825600	Weak transcription	HUVEC	blood vessel
35	chr2:38814600-38824200	Weak transcription	Fetal Brain Female	brain
36	chr2:38815200-38824000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:38815200-38824000	Weak transcription	Fetal Intestine Large	intestine
38	chr2:38815200-38825200	Weak transcription	Gastric	stomach
39	chr2:38815200-38825400	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:38815200-38825800	Weak transcription	Fetal Brain Male	brain
41	chr2:38815400-38824200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:38815400-38825400	Weak transcription	Fetal Kidney	kidney
43	chr2:38815600-38821800	Weak transcription	Lung	lung
44	chr2:38816800-38821800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr2:38817400-38820600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr2:38817400-38824000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr2:38817600-38824200	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:38818000-38823200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr2:38818000-38825400	Weak transcription	Brain Substantia Nigra	brain
50	chr2:38818200-38821800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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