Variant report

Variant	rs7025939
Chromosome Location	chr9:136737118-136737119
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136682372..136685091-chr9:136736448..136738979,2	MCF-7	breast:
2	chr9:136733619..136743972-chr9:136852076..136861381,50	MCF-7	breast:
3	chr17:57919485..57922365-chr9:136736871..136739755,2	MCF-7	breast:
4	chr9:136737105..136739674-chr9:136778546..136781444,2	MCF-7	breast:
5	chr9:136698753..136701712-chr9:136736999..136741089,4	MCF-7	breast:
6	chr9:136736947..136741233-chr9:136835339..136839101,5	MCF-7	breast:
7	chr9:136736139..136748779-chr9:136853521..136861128,82	MCF-7	breast:
8	chr9:136655680..136661750-chr9:136735179..136740692,8	MCF-7	breast:
9	chr9:136649018..136654096-chr9:136736895..136740406,5	MCF-7	breast:
10	chr9:136701985..136719064-chr9:136732605..136742545,35	MCF-7	breast:
11	chr9:136720764..136723622-chr9:136736992..136740613,4	MCF-7	breast:
12	chr9:136736821..136740635-chr9:136999583..137001478,3	MCF-7	breast:
13	chr9:136734394..136737190-chr9:136823584..136826132,2	MCF-7	breast:
14	chr9:136658148..136661518-chr9:136735926..136740986,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction
ENSG00000196363	Chromatin interaction
ENSG00000273249	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10114138	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10114514	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10116085	0.97[ASN][1000 genomes]
rs10217798	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821527	0.87[CEU][hapmap]
rs10821528	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821530	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10821531	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993823	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs10993826	0.87[CEU][hapmap]
rs10993836	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs10993839	0.85[EUR][1000 genomes]
rs12001216	0.82[CEU][hapmap]
rs12002290	1.00[CHB][hapmap]
rs12376343	0.87[EUR][1000 genomes]
rs12377799	0.80[EUR][1000 genomes]
rs2073830	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2073929	0.87[CEU][hapmap]
rs2156323	0.93[CEU][hapmap]
rs2260095	0.81[CEU][hapmap]
rs2486350	0.86[CEU][hapmap]
rs2486351	0.87[CEU][hapmap]
rs2510254	0.87[CEU][hapmap]
rs3780737	0.87[CEU][hapmap];0.84[TSI][hapmap]
rs3780739	0.88[EUR][1000 genomes]
rs3780741	0.87[EUR][1000 genomes]
rs3819500	0.87[CEU][hapmap]
rs3819502	0.87[CEU][hapmap]
rs61034217	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7021948	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7022082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7025684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7025729	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7026235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7034805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7038256	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046381	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs739466	0.81[CEU][hapmap]
rs7852459	1.00[CHB][hapmap]
rs7853626	0.87[CEU][hapmap]
rs9657700	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9657701	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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
rs7025939	LCN8	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

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	chr9:136727800-136738400	Weak transcription	HepG2	liver
4	chr9:136727800-136739000	Weak transcription	NHLF	lung
5	chr9:136729600-136737600	Weak transcription	HSMM	muscle
6	chr9:136729600-136780000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:136729800-136762600	Weak transcription	Right Ventricle	heart
8	chr9:136730000-136738400	Weak transcription	Fetal Intestine Large	intestine
9	chr9:136730000-136739200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr9:136730800-136738400	Weak transcription	A549	lung
11	chr9:136731200-136738400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:136731200-136738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr9:136731200-136738400	Weak transcription	Osteobl	bone
14	chr9:136731800-136739800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:136733800-136737400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr9:136735400-136737200	Weak transcription	Fetal Muscle Leg	muscle
17	chr9:136735400-136738600	Weak transcription	Right Atrium	heart
18	chr9:136735600-136738400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:136735600-136739400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr9:136735600-136740600	Weak transcription	Brain Germinal Matrix	brain
21	chr9:136735600-136744200	Weak transcription	Fetal Brain Male	brain
22	chr9:136735600-136747400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr9:136735800-136737200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr9:136735800-136737600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr9:136735800-136738400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr9:136735800-136738400	Weak transcription	Fetal Brain Female	brain
27	chr9:136735800-136738400	Weak transcription	Fetal Lung	lung
28	chr9:136735800-136738400	Weak transcription	Fetal Thymus	thymus
29	chr9:136735800-136739800	Weak transcription	Liver	Liver
30	chr9:136735800-136741400	Weak transcription	Gastric	stomach
31	chr9:136735800-136742400	Weak transcription	GM12878-XiMat	blood
32	chr9:136736000-136737600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:136736000-136737800	Weak transcription	Lung	lung
34	chr9:136736000-136738400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:136736000-136738800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:136736000-136739200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr9:136736000-136760000	Weak transcription	Primary B cells from cord blood	blood
38	chr9:136736400-136738000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:136736400-136738400	Strong transcription	Fetal Intestine Small	intestine
40	chr9:136736400-136745200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr9:136736600-136737800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:136736600-136739200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:136736800-136737600	Enhancers	NHEK	skin
44	chr9:136736800-136737800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr9:136736800-136738200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:136736800-136738600	Enhancers	HMEC	breast
47	chr9:136736800-136756200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr9:136737000-136737200	Weak transcription	Fetal Stomach	stomach
49	chr9:136737000-136737200	Transcr. at gene 5' and 3'	Hela-S3	cervix
50	chr9:136737000-136737400	Weak transcription	Pancreas	Pancrea

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