Variant report

Variant	rs12377799
Chromosome Location	chr9:136727218-136727219
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136725437..136727832-chr9:136728228..136730381,2	K562	blood:
2	chr9:136724408..136730266-chr9:136853620..136859994,16	MCF-7	breast:
3	chr9:136723768..136727391-chr9:136738428..136742111,4	MCF-7	breast:
4	chr9:136700961..136707109-chr9:136726164..136730903,8	MCF-7	breast:
5	chr9:136726221..136733157-chr9:136853321..136860155,11	MCF-7	breast:
6	chr9:136655858..136660240-chr9:136726638..136729094,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10114514	0.80[EUR][1000 genomes]
rs10217798	0.80[EUR][1000 genomes]
rs10821526	0.90[ASN][1000 genomes]
rs10821530	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10993820	0.96[ASN][1000 genomes]
rs10993822	1.00[ASN][1000 genomes]
rs10993823	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993824	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993826	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10993828	1.00[ASN][1000 genomes]
rs10993829	1.00[ASN][1000 genomes]
rs10993830	1.00[ASN][1000 genomes]
rs10993832	1.00[ASN][1000 genomes]
rs10993836	0.82[AMR][1000 genomes]
rs10993839	0.82[AMR][1000 genomes]
rs12000549	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12005762	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12341505	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12376343	0.85[AMR][1000 genomes]
rs1557679	0.90[ASN][1000 genomes]
rs17663678	1.00[ASN][1000 genomes]
rs2073928	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2073929	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2073930	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2156323	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2260095	0.93[ASN][1000 genomes]
rs2261150	0.90[ASN][1000 genomes]
rs2428123	0.90[ASN][1000 genomes]
rs2428124	1.00[ASN][1000 genomes]
rs2428126	0.90[ASN][1000 genomes]
rs2428129	0.90[ASN][1000 genomes]
rs2486350	0.90[ASN][1000 genomes]
rs2486351	0.90[ASN][1000 genomes]
rs2502765	0.90[ASN][1000 genomes]
rs2510254	0.90[ASN][1000 genomes]
rs28436700	0.90[ASN][1000 genomes]
rs35711919	1.00[ASN][1000 genomes]
rs35776936	1.00[ASN][1000 genomes]
rs3780739	0.82[AMR][1000 genomes]
rs3780741	0.85[AMR][1000 genomes]
rs3819500	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3819502	0.90[ASN][1000 genomes]
rs3819503	0.88[ASN][1000 genomes]
rs3819504	1.00[ASN][1000 genomes]
rs3819505	1.00[ASN][1000 genomes]
rs55646136	1.00[ASN][1000 genomes]
rs55939286	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56745684	0.90[ASN][1000 genomes]
rs56868628	0.88[ASN][1000 genomes]
rs58816065	0.90[ASN][1000 genomes]
rs67484139	1.00[ASN][1000 genomes]
rs7025939	0.80[EUR][1000 genomes]
rs7026235	0.80[EUR][1000 genomes]
rs7038256	0.80[EUR][1000 genomes]
rs72762854	1.00[ASN][1000 genomes]
rs72762864	1.00[ASN][1000 genomes]
rs7853626	1.00[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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136675200-136728400	Weak transcription	Esophagus	oesophagus
2	chr9:136705800-136729400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:136709000-136728600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:136710000-136727400	Weak transcription	Brain Substantia Nigra	brain
5	chr9:136710800-136728600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr9:136711400-136737800	Weak transcription	NH-A	brain
7	chr9:136711600-136727400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:136714600-136729400	Weak transcription	NHEK	skin
9	chr9:136717200-136728600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr9:136718400-136727400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:136719400-136728200	Weak transcription	NHDF-Ad	bronchial
12	chr9:136719600-136727400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:136719600-136727800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:136720600-136727800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:136721200-136727400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:136721200-136727600	Weak transcription	Right Ventricle	heart
17	chr9:136721200-136728000	Weak transcription	Right Atrium	heart
18	chr9:136721200-136728600	Weak transcription	HSMMtube	muscle
19	chr9:136721200-136729800	Weak transcription	A549	lung
20	chr9:136721400-136727600	Weak transcription	Left Ventricle	heart
21	chr9:136721400-136728400	Weak transcription	Fetal Lung	lung
22	chr9:136721400-136738600	Weak transcription	HUVEC	blood vessel
23	chr9:136721600-136728400	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:136721800-136727800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:136722000-136727600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr9:136722000-136728400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:136722000-136728800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:136722200-136727400	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr9:136722400-136727400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr9:136722400-136728000	Strong transcription	Fetal Intestine Small	intestine
31	chr9:136722400-136728200	Strong transcription	Fetal Stomach	stomach
32	chr9:136723000-136727400	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:136723400-136727800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:136723400-136727800	Strong transcription	HepG2	liver
35	chr9:136723800-136727800	Strong transcription	NHLF	lung
36	chr9:136723800-136730000	Weak transcription	Hela-S3	cervix
37	chr9:136724600-136729000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:136725600-136728600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr9:136725600-136729600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr9:136725800-136728600	Enhancers	Fetal Brain Male	brain
41	chr9:136725800-136730000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr9:136726000-136727400	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:136726000-136727800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr9:136726200-136728000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr9:136726200-136728600	Enhancers	Fetal Brain Female	brain
46	chr9:136726200-136729200	Enhancers	Brain Germinal Matrix	brain
47	chr9:136726200-136735400	Weak transcription	Aorta	Aorta
48	chr9:136726400-136727400	Weak transcription	Brain Anterior Caudate	brain
49	chr9:136726400-136727800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:136726400-136728600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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