Variant report

Variant	rs2510238
Chromosome Location	chr9:136699229-136699230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136698753..136701712-chr9:136736999..136741089,4	MCF-7	breast:
2	chr9:136694438..136696917-chr9:136696926..136699565,2	MCF-7	breast:
3	chr9:136697564..136700865-chr9:136704214..136707852,3	MCF-7	breast:
4	chr9:136694512..136703388-chr9:136855005..136859658,12	MCF-7	breast:
5	chr9:136658683..136660342-chr9:136699165..136701047,2	MCF-7	breast:
6	chr9:136697764..136700285-chr9:136729110..136730934,2	MCF-7	breast:
7	chr9:136697949..136700533-chr9:136718223..136719724,2	MCF-7	breast:
8	chr9:136698344..136701067-chr9:136709180..136711930,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10821526	0.89[CEU][hapmap]
rs10993816	0.88[ASN][1000 genomes]
rs10993820	0.95[CEU][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs10993829	0.88[CEU][hapmap]
rs10993830	0.89[CEU][hapmap]
rs10993832	0.89[CEU][hapmap]
rs10993836	1.00[JPT][hapmap]
rs12344583	0.84[CEU][hapmap]
rs17663678	0.89[CEU][hapmap]
rs2260095	0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3780741	1.00[JPT][hapmap]
rs3819503	0.89[CEU][hapmap]
rs7023551	0.89[CEU][hapmap];0.81[TSI][hapmap]

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	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1035272	chr9:136665308-136772256	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2510238	LCN8	cis	parietal	SCAN
rs2510238	BAT2L1	cis	parietal	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136658800-136705400	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:136659000-136702200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr9:136673200-136705000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr9:136675200-136728400	Weak transcription	Esophagus	oesophagus
5	chr9:136675400-136703200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:136675400-136709400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr9:136675600-136704800	Weak transcription	Adipose Nuclei	Adipose
8	chr9:136676000-136699800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:136677000-136705000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:136682200-136701000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:136683800-136705000	Weak transcription	NHDF-Ad	bronchial
12	chr9:136684200-136704800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr9:136686000-136709600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:136686600-136705000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:136687600-136705000	Weak transcription	HSMMtube	muscle
16	chr9:136689200-136704800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr9:136691400-136704800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr9:136691400-136705000	Weak transcription	Fetal Kidney	kidney
19	chr9:136691800-136703200	Weak transcription	Colonic Mucosa	Colon
20	chr9:136691800-136704800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr9:136692000-136700600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr9:136692000-136700600	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:136692000-136704800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:136692000-136704800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:136692000-136705000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:136692000-136705000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:136692000-136709800	Weak transcription	NH-A	brain
28	chr9:136692200-136699800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:136692200-136700600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:136692200-136705000	Weak transcription	Left Ventricle	heart
31	chr9:136692200-136705200	Weak transcription	Right Atrium	heart
32	chr9:136692400-136700800	Strong transcription	Fetal Intestine Small	intestine
33	chr9:136692400-136704800	Weak transcription	Fetal Lung	lung
34	chr9:136693400-136699600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr9:136693600-136699600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:136693600-136699600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:136693600-136699600	Strong transcription	Liver	Liver
38	chr9:136693600-136699800	Strong transcription	Fetal Stomach	stomach
39	chr9:136693600-136702200	Strong transcription	HepG2	liver
40	chr9:136693800-136699800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:136693800-136700000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:136693800-136703600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr9:136694000-136700000	Strong transcription	Fetal Intestine Large	intestine
44	chr9:136694600-136700800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr9:136695800-136699600	Weak transcription	Brain Germinal Matrix	brain
46	chr9:136696000-136700000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:136696200-136704800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr9:136696200-136704800	Weak transcription	HSMM	muscle
49	chr9:136696400-136699800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr9:136696800-136699800	Strong transcription	Gastric	stomach

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