Variant report

Variant	rs72907906
Chromosome Location	chr2:38821352-38821353
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr2:38821248-38821623	K562	blood:	n/a	n/a
2	POLR2A	chr2:38821240-38821636	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

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	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
8	chr2:38778255..38779937-chr2:38819083..38821616,2	K562	blood:
9	chr2:38820056..38822885-chr2:38968180..38969856,2	MCF-7	breast:

No data

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

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1543881	0.81[AMR][1000 genomes]
rs17022945	0.81[AFR][1000 genomes]
rs17603782	0.81[AMR][1000 genomes]
rs55773228	0.81[AFR][1000 genomes]
rs6710613	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6748685	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905880	0.81[AFR][1000 genomes]
rs72907918	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907929	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73929052	0.81[AMR][1000 genomes]
rs7580657	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7594264	0.81[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:115 , 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	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:38798800-38822000	Weak transcription	NHEK	skin
11	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:38808200-38824400	Weak transcription	Hela-S3	cervix
14	chr2:38808800-38821800	Weak transcription	HMEC	breast
15	chr2:38808800-38825200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:38808800-38825400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
20	chr2:38809000-38824200	Weak transcription	Liver	Liver
21	chr2:38809000-38825600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:38809400-38825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:38810000-38827600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr2:38812600-38823800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:38813000-38821800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr2:38813000-38821800	Weak transcription	Adipose Nuclei	Adipose
28	chr2:38813000-38823800	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:38813200-38826000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr2:38813400-38827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:38813800-38825400	Weak transcription	Primary T cells from cord blood	blood
32	chr2:38814400-38825200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:38814400-38825600	Weak transcription	HUVEC	blood vessel
34	chr2:38814600-38824200	Weak transcription	Fetal Brain Female	brain
35	chr2:38815200-38824000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr2:38815200-38824000	Weak transcription	Fetal Intestine Large	intestine
37	chr2:38815200-38825200	Weak transcription	Gastric	stomach
38	chr2:38815200-38825400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:38815200-38825800	Weak transcription	Fetal Brain Male	brain
40	chr2:38815400-38824200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:38815400-38825400	Weak transcription	Fetal Kidney	kidney
42	chr2:38815600-38821800	Weak transcription	Lung	lung
43	chr2:38816800-38821800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:38817400-38824000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:38817600-38824200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr2:38818000-38823200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr2:38818000-38825400	Weak transcription	Brain Substantia Nigra	brain
48	chr2:38818200-38821800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr2:38818200-38821800	Weak transcription	Fetal Stomach	stomach
50	chr2:38818200-38823800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links