Variant report

Variant	rs3780741
Chromosome Location	chr9:136740086-136740087
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:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136728244..136728911-chr9:136739593..136740116,2	MCF-7	breast:
2	chr9:136695295..136698632-chr9:136737582..136741114,3	MCF-7	breast:
3	chr9:136737561..136740251-chr9:136741491..136743722,2	K562	blood:
4	chr9:136738620..136740987-chr9:136829938..136833023,3	MCF-7	breast:
5	chr2:238395363..238396972-chr9:136738845..136741262,2	MCF-7	breast:
6	chr9:136644385..136647944-chr9:136738272..136741517,4	MCF-7	breast:
7	chr9:136733619..136743972-chr9:136852076..136861381,50	MCF-7	breast:
8	chr9:136674892..136676991-chr9:136737991..136740534,2	MCF-7	breast:
9	chr9:136699416..136701767-chr9:136738556..136740332,2	MCF-7	breast:
10	chr9:136698753..136701712-chr9:136736999..136741089,4	MCF-7	breast:
11	chr9:136736947..136741233-chr9:136835339..136839101,5	MCF-7	breast:
12	chr9:136738035..136740400-chr9:136850110..136852807,2	MCF-7	breast:
13	chr9:136737400..136743457-chr9:136819359..136829756,12	MCF-7	breast:
14	chr9:136736139..136748779-chr9:136853521..136861128,82	MCF-7	breast:
15	chr9:136655680..136661750-chr9:136735179..136740692,8	MCF-7	breast:
16	chr9:136649018..136654096-chr9:136736895..136740406,5	MCF-7	breast:
17	chr9:136701985..136719064-chr9:136732605..136742545,35	MCF-7	breast:
18	chr9:136738615..136741064-chr9:136782245..136785156,2	MCF-7	breast:
19	chr9:136723768..136727391-chr9:136738428..136742111,4	MCF-7	breast:
20	chr9:136738092..136740992-chr9:136890169..136892007,2	MCF-7	breast:
21	chr9:136720764..136723622-chr9:136736992..136740613,4	MCF-7	breast:
22	chr9:136707781..136709506-chr9:136739982..136742386,2	MCF-7	breast:
23	chr9:136736821..136740635-chr9:136999583..137001478,3	MCF-7	breast:
24	chr9:136685827..136689292-chr9:136739053..136741402,3	MCF-7	breast:
25	chr9:136703509..136705855-chr9:136737754..136741325,4	MCF-7	breast:
26	chr17:62222323..62224365-chr9:136738954..136740664,2	MCF-7	breast:
27	chr9:136737792..136741016-chr9:136774631..136778412,3	MCF-7	breast:
28	chr9:136658148..136661518-chr9:136735926..136740986,7	MCF-7	breast:
29	chr9:136739328..136742123-chr9:136841796..136845434,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000196363	Chromatin interaction
ENSG00000160293	Chromatin interaction
ENSG00000235106	Chromatin interaction
ENSG00000199753	Chromatin interaction
ENSG00000115648	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000273249	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10114138	0.87[EUR][1000 genomes]
rs10114514	0.87[EUR][1000 genomes]
rs10217798	0.87[EUR][1000 genomes]
rs10821527	0.80[CEU][hapmap]
rs10821530	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10993823	0.82[AMR][1000 genomes]
rs10993824	0.82[AMR][1000 genomes]
rs10993826	0.80[CEU][hapmap]
rs10993836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993839	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993842	0.81[LWK][hapmap]
rs12001180	0.82[CEU][hapmap]
rs12001216	0.91[CEU][hapmap]
rs12376343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12377799	0.85[AMR][1000 genomes]
rs2073830	0.80[CEU][hapmap]
rs2073929	0.80[CEU][hapmap]
rs2073930	0.82[AMR][1000 genomes]
rs2156323	1.00[MEX][hapmap];0.82[AMR][1000 genomes]
rs2486351	0.80[CEU][hapmap]
rs2510238	1.00[JPT][hapmap]
rs2510254	0.80[CEU][hapmap]
rs3780737	0.80[CEU][hapmap]
rs3780739	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3819500	0.80[CEU][hapmap]
rs3819502	0.80[CEU][hapmap]
rs7022082	0.87[EUR][1000 genomes]
rs7025684	0.87[EUR][1000 genomes]
rs7025729	0.87[EUR][1000 genomes]
rs7025939	0.87[EUR][1000 genomes]
rs7026235	0.87[EUR][1000 genomes]
rs7034805	0.87[EUR][1000 genomes]
rs7038256	0.87[EUR][1000 genomes]
rs7046381	0.87[EUR][1000 genomes]
rs7852459	0.87[CEU][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs7853626	0.80[CEU][hapmap]
rs7869522	0.91[CEU][hapmap]
rs9657701	0.87[EUR][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	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	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
3	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
4	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
5	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
6	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
7	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3780741	LCN8	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136729600-136780000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr9:136729800-136762600	Weak transcription	Right Ventricle	heart
3	chr9:136735600-136740600	Weak transcription	Brain Germinal Matrix	brain
4	chr9:136735600-136744200	Weak transcription	Fetal Brain Male	brain
5	chr9:136735600-136747400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr9:136735800-136741400	Weak transcription	Gastric	stomach
7	chr9:136735800-136742400	Weak transcription	GM12878-XiMat	blood
8	chr9:136736000-136760000	Weak transcription	Primary B cells from cord blood	blood
9	chr9:136736400-136745200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr9:136736800-136756200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr9:136737000-136743000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr9:136737200-136742800	Enhancers	Fetal Muscle Leg	muscle
13	chr9:136737200-136749000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr9:136737600-136740600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr9:136737800-136740200	Enhancers	Lung	lung
16	chr9:136737800-136740400	Enhancers	Spleen	Spleen
17	chr9:136738000-136740800	Enhancers	Placenta	Placenta
18	chr9:136738200-136740400	Flanking Active TSS	NHEK	skin
19	chr9:136738200-136740600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr9:136738200-136743000	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr9:136738400-136740200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:136738400-136740200	Flanking Active TSS	Hela-S3	cervix
23	chr9:136738400-136740600	Enhancers	Fetal Intestine Large	intestine
24	chr9:136738400-136740600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr9:136738400-136741000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:136738400-136741000	Enhancers	Fetal Stomach	stomach
27	chr9:136738400-136741400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr9:136738400-136741400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:136738400-136741800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr9:136738400-136742000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr9:136738400-136742400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr9:136738400-136742600	Enhancers	Esophagus	oesophagus
33	chr9:136738400-136743800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr9:136738400-136744800	Genic enhancers	Fetal Intestine Small	intestine
35	chr9:136738600-136740200	Enhancers	HUVEC	blood vessel
36	chr9:136738800-136740400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:136738800-136741200	Weak transcription	Brain Substantia Nigra	brain
38	chr9:136738800-136742000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr9:136738800-136744400	Weak transcription	Fetal Brain Female	brain
40	chr9:136738800-136746000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr9:136738800-136746400	Weak transcription	Right Atrium	heart
42	chr9:136739000-136740200	Enhancers	Muscle Satellite Cultured Cells	--
43	chr9:136739000-136740200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:136739000-136740600	Enhancers	NH-A	brain
45	chr9:136739000-136741400	Enhancers	HSMMtube	muscle
46	chr9:136739200-136740200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr9:136739200-136741800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr9:136739200-136742400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:136739400-136740200	Enhancers	Duodenum Mucosa	Duodenum
50	chr9:136739400-136741800	Weak transcription	Brain Hippocampus Middle	brain

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