Variant report

Variant	rs3780737
Chromosome Location	chr9:136732767-136732768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136729185..136731068-chr9:136732644..136734219,2	K562	blood:
2	chr9:136732119..136736339-chr9:136737588..136739921,3	K562	blood:
3	chr9:136701985..136719064-chr9:136732605..136742545,35	MCF-7	breast:
4	chr9:136726221..136733157-chr9:136853321..136860155,11	MCF-7	breast:
5	chr9:136730272..136735488-chr9:136855005..136861125,10	MCF-7	breast:
6	chr9:136647424..136648976-chr9:136729858..136732826,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10739995	0.85[EUR][1000 genomes]
rs10821527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821528	0.96[EUR][1000 genomes]
rs10821531	0.85[EUR][1000 genomes]
rs10993826	0.87[CEU][hapmap];1.00[MEX][hapmap]
rs10993836	0.87[CEU][hapmap]
rs12001216	0.91[CEU][hapmap]
rs12344583	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2073830	0.87[CEU][hapmap];0.96[EUR][1000 genomes]
rs2073929	0.87[CEU][hapmap];1.00[MEX][hapmap]
rs2260095	0.81[CEU][hapmap]
rs2486350	0.87[CEU][hapmap]
rs2486351	0.87[CEU][hapmap]
rs2510254	0.87[CEU][hapmap]
rs3780739	0.80[CEU][hapmap]
rs3780741	0.80[CEU][hapmap]
rs3819500	0.87[CEU][hapmap];1.00[MEX][hapmap]
rs3819502	0.87[CEU][hapmap]
rs57520738	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61034217	0.96[EUR][1000 genomes]
rs6479627	0.89[ASN][1000 genomes]
rs7021948	0.94[EUR][1000 genomes]
rs7023551	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs7025939	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs7038256	0.87[CEU][hapmap];0.86[CHD][hapmap];0.84[TSI][hapmap]
rs7044185	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs739466	0.94[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7852459	0.82[EUR][1000 genomes]
rs7853626	0.87[CEU][hapmap]
rs7859624	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7869522	0.82[CEU][hapmap]
rs9657700	0.94[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
rs3780737	LCN8	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136711400-136737800	Weak transcription	NH-A	brain
2	chr9:136721400-136738600	Weak transcription	HUVEC	blood vessel
3	chr9:136726200-136735400	Weak transcription	Aorta	Aorta
4	chr9:136726600-136735200	Weak transcription	Gastric	stomach
5	chr9:136727800-136738400	Weak transcription	HepG2	liver
6	chr9:136727800-136739000	Weak transcription	NHLF	lung
7	chr9:136729200-136734400	Weak transcription	Primary B cells from cord blood	blood
8	chr9:136729600-136734800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr9:136729600-136735000	Weak transcription	Left Ventricle	heart
10	chr9:136729600-136737600	Weak transcription	HSMM	muscle
11	chr9:136729600-136780000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:136729800-136762600	Weak transcription	Right Ventricle	heart
13	chr9:136730000-136735200	Weak transcription	Right Atrium	heart
14	chr9:136730000-136735400	Weak transcription	Spleen	Spleen
15	chr9:136730000-136736800	Weak transcription	HMEC	breast
16	chr9:136730000-136737000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:136730000-136738400	Weak transcription	Fetal Intestine Large	intestine
18	chr9:136730000-136739200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:136730200-136733800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:136730200-136734800	Weak transcription	Pancreas	Pancrea
21	chr9:136730800-136738400	Weak transcription	A549	lung
22	chr9:136731000-136734800	Weak transcription	NHEK	skin
23	chr9:136731200-136734800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr9:136731200-136737000	Weak transcription	Hela-S3	cervix
25	chr9:136731200-136738400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:136731200-136738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr9:136731200-136738400	Weak transcription	Osteobl	bone
28	chr9:136731400-136734200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr9:136731400-136734400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:136731400-136734400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:136731400-136734800	Weak transcription	Fetal Brain Female	brain
32	chr9:136731400-136734800	Strong transcription	Fetal Intestine Small	intestine
33	chr9:136731400-136734800	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:136731400-136735000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:136731600-136734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:136731600-136734800	Weak transcription	Brain Germinal Matrix	brain
37	chr9:136731600-136735000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:136731600-136735000	Weak transcription	GM12878-XiMat	blood
39	chr9:136731600-136735200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr9:136731800-136739800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:136732000-136734000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr9:136732200-136733000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr9:136732200-136733000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:136732200-136733800	Strong transcription	Fetal Stomach	stomach
45	chr9:136732400-136735200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:136732600-136734800	Weak transcription	Liver	Liver
47	chr9:136732600-136736400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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