Variant report

Variant	rs6769934
Chromosome Location	chr3:136269396-136269397
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:136268066..136271170-chr3:136469546..136471486,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261758	Chromatin interaction
ENSG00000118007	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs16843991	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28396702	0.81[EUR][1000 genomes]
rs34165586	0.82[EUR][1000 genomes]
rs34962604	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35375192	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35644083	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3932048	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4336059	0.85[EUR][1000 genomes]
rs4402873	0.84[EUR][1000 genomes]
rs55993001	0.82[EUR][1000 genomes]
rs56040643	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56047785	0.85[EUR][1000 genomes]
rs56125228	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs59931907	0.85[EUR][1000 genomes]
rs6439642	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66810260	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6766450	0.82[EUR][1000 genomes]
rs6782151	0.85[EUR][1000 genomes]
rs6789541	0.84[EUR][1000 genomes]
rs6789761	0.94[EUR][1000 genomes]
rs6799368	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804194	0.81[EUR][1000 genomes]
rs6806795	0.88[EUR][1000 genomes]
rs7612160	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7615706	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621017	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7621970	0.85[EUR][1000 genomes]
rs7623824	0.84[EUR][1000 genomes]
rs7627292	0.86[EUR][1000 genomes]
rs7644471	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648591	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9812319	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9819496	0.81[EUR][1000 genomes]
rs9832572	0.86[EUR][1000 genomes]
rs9834631	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9850383	0.84[EUR][1000 genomes]
rs9858457	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9866535	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877786	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv877519	chr3:136035737-136279390	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	nsv877524	chr3:136112109-136295283	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	nsv877528	chr3:136209550-136295283	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv591850	chr3:136209550-136300732	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	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
14	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

No data

Chromatin state (count:68 , 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	chr3:136195400-136278800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:136212200-136323400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:136213000-136326600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr3:136246600-136286200	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:136247200-136319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:136247200-136334800	Weak transcription	Aorta	Aorta
8	chr3:136247400-136270600	Weak transcription	Fetal Thymus	thymus
9	chr3:136248200-136349200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:136251400-136319000	Weak transcription	Duodenum Mucosa	Duodenum
11	chr3:136251600-136270400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:136251600-136284400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:136251600-136284400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:136251600-136289400	Weak transcription	Adipose Nuclei	Adipose
15	chr3:136251600-136322400	Weak transcription	Liver	Liver
16	chr3:136251800-136284800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr3:136252000-136270000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr3:136252600-136284800	Weak transcription	Left Ventricle	heart
19	chr3:136252600-136320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:136252800-136305600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:136252800-136314800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:136255200-136294000	Weak transcription	Primary T cells from cord blood	blood
23	chr3:136255800-136291600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:136257600-136270000	Weak transcription	Fetal Stomach	stomach
25	chr3:136257600-136282800	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:136258000-136269800	Weak transcription	Fetal Intestine Small	intestine
27	chr3:136258200-136275400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:136259000-136269800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:136261000-136269600	Weak transcription	Dnd41	blood
30	chr3:136263000-136327200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:136263200-136272000	Weak transcription	Stomach Mucosa	stomach
32	chr3:136263800-136277600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:136265000-136271400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:136265000-136272800	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:136265000-136294200	Weak transcription	Fetal Lung	lung
36	chr3:136265200-136278600	Weak transcription	Brain Substantia Nigra	brain
37	chr3:136265400-136314800	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:136265800-136278400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:136266000-136275400	Weak transcription	Ovary	ovary
40	chr3:136266400-136315600	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:136266600-136271600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:136266600-136275200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr3:136266600-136278200	Weak transcription	HMEC	breast
44	chr3:136266600-136284200	Weak transcription	Primary B cells from cord blood	blood
45	chr3:136266600-136284600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:136266600-136284800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:136266600-136291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr3:136266600-136314600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr3:136266600-136316200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr3:136266800-136271600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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