Variant report

Variant	rs9839137
Chromosome Location	chr3:136304262-136304263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136303371..136305169-chr3:136469440..136472893,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12695649	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13071220	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13092193	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13096466	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13100192	0.82[EUR][1000 genomes]
rs13321721	0.81[AMR][1000 genomes]
rs13326151	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13433688	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13434116	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17298525	0.83[AMR][1000 genomes]
rs17364492	0.82[AMR][1000 genomes]
rs28390205	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28472992	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28641809	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28718456	0.87[AMR][1000 genomes]
rs28750366	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28811905	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28877020	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34135127	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34168675	0.87[AMR][1000 genomes]
rs34804893	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35326900	0.87[AMR][1000 genomes]
rs35428413	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35899944	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4038586	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs67145204	0.85[EUR][1000 genomes]
rs67382287	0.83[EUR][1000 genomes]
rs6767889	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6768743	0.87[AMR][1000 genomes]
rs6771002	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6773949	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6774964	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6775314	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs67949818	0.83[AMR][1000 genomes]
rs6806123	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71310215	0.81[EUR][1000 genomes]
rs71336069	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73230043	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7612425	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9813691	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9818056	0.82[AMR][1000 genomes]
rs9820717	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9828088	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9847427	0.84[EUR][1000 genomes]
rs9857833	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9857966	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9869630	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9875770	0.84[EUR][1000 genomes]
rs9878078	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9881831	0.84[EUR][1000 genomes]
rs9883189	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948461	chr3:135969755-136349636	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv877520	chr3:136056861-136310985	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv877521	chr3:136069286-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv877523	chr3:136088038-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv520012	chr3:136088038-136314119	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv877525	chr3:136112109-136310985	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv877526	chr3:136149139-136310985	ZNF genes & repeats Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv877527	chr3:136182053-136310985	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv460861	chr3:136222954-136425600	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv591851	chr3:136222954-136425600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv1794138	chr3:136300732-136332204	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:136176400-136314200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
6	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
8	chr3:136251600-136322400	Weak transcription	Liver	Liver
9	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:136265400-136314800	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:136266400-136315600	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:136266600-136314600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:136266600-136316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:136266800-136314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr3:136268200-136351200	Weak transcription	Esophagus	oesophagus
19	chr3:136271200-136331400	Weak transcription	NHDF-Ad	bronchial
20	chr3:136272600-136335600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:136274200-136314000	Weak transcription	GM12878-XiMat	blood
22	chr3:136277800-136315200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:136280000-136323000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:136283600-136314600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr3:136283800-136341800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:136284400-136337800	Weak transcription	Fetal Kidney	kidney
27	chr3:136285000-136307200	Weak transcription	Lung	lung
28	chr3:136285000-136314800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:136285200-136335400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:136285400-136313600	Weak transcription	Left Ventricle	heart
31	chr3:136286400-136305200	Weak transcription	Fetal Thymus	thymus
32	chr3:136286600-136314600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr3:136286800-136307200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:136286800-136322600	Weak transcription	Placenta	Placenta
35	chr3:136286800-136343600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:136287200-136335400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:136287400-136305200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:136288000-136304800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:136289600-136341800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:136290000-136351600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:136290400-136305600	Weak transcription	Gastric	stomach
42	chr3:136290400-136315000	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:136292000-136307000	Weak transcription	Fetal Muscle Leg	muscle
44	chr3:136292200-136307200	Weak transcription	Thymus	Thymus
45	chr3:136293000-136306000	Weak transcription	Fetal Stomach	stomach
46	chr3:136293200-136306600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:136294400-136305400	Weak transcription	Fetal Intestine Small	intestine
48	chr3:136294400-136314600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:136294800-136319600	Weak transcription	Fetal Lung	lung
50	chr3:136295200-136307200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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