Variant report

Variant	rs13097830
Chromosome Location	chr3:99585125-99585126
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99582999..99585506-chr3:99592416..99595464,3	MCF-7	breast:
2	chr3:99584236..99588094-chr3:99589040..99591682,4	MCF-7	breast:
3	chr3:99574024..99577676-chr3:99581622..99586745,5	K562	blood:
4	chr3:99584410..99586958-chr3:99739042..99741066,2	K562	blood:
5	chr3:99582314..99585905-chr3:99590964..99594499,4	MCF-7	breast:
6	chr3:99582343..99586390-chr3:99587207..99589734,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs13060898	1.00[JPT][hapmap]
rs13063594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13073356	1.00[JPT][hapmap]
rs13074107	1.00[JPT][hapmap]
rs13076199	0.87[EUR][1000 genomes]
rs13081855	1.00[JPT][hapmap]
rs13082013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084413	1.00[CEU][hapmap]
rs13089461	0.87[EUR][1000 genomes]
rs13095282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13100490	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17778253	1.00[JPT][hapmap]
rs34174004	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34571898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34971126	0.82[AMR][1000 genomes]
rs35074168	1.00[AFR][1000 genomes]
rs35098023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35669249	1.00[AFR][1000 genomes]
rs36077012	0.87[EUR][1000 genomes]
rs62283494	1.00[AFR][1000 genomes]
rs62283538	0.82[EUR][1000 genomes]
rs6788894	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6791889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7626245	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7636514	1.00[JPT][hapmap]
rs7647466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7649862	1.00[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99537200-99594400	Weak transcription	Esophagus	oesophagus
2	chr3:99563200-99593600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:99565600-99589400	Weak transcription	K562	blood
4	chr3:99569000-99589600	Weak transcription	Colonic Mucosa	Colon
5	chr3:99573200-99594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:99573400-99589200	Genic enhancers	HepG2	liver
7	chr3:99574400-99590000	Weak transcription	Liver	Liver
8	chr3:99575000-99587000	Weak transcription	Pancreas	Pancrea
9	chr3:99575000-99593600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:99575200-99587000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:99576000-99587600	Genic enhancers	NHDF-Ad	bronchial
12	chr3:99577400-99587200	Weak transcription	Brain Anterior Caudate	brain
13	chr3:99578200-99585400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:99579200-99591000	Genic enhancers	NH-A	brain
15	chr3:99579400-99587000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:99579400-99591000	Weak transcription	Fetal Lung	lung
17	chr3:99579600-99585200	Weak transcription	Small Intestine	intestine
18	chr3:99579600-99585400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:99579600-99592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:99580400-99585200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:99580400-99585200	Weak transcription	Fetal Kidney	kidney
22	chr3:99580400-99585400	Strong transcription	Fetal Muscle Leg	muscle
23	chr3:99580600-99585200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:99580600-99587000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:99580600-99587600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:99580800-99590800	Weak transcription	Lung	lung
27	chr3:99581200-99589200	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:99581400-99585400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:99581400-99585400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:99581400-99594000	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:99581800-99589600	Weak transcription	Gastric	stomach
32	chr3:99582000-99587200	Weak transcription	Spleen	Spleen
33	chr3:99582000-99589400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:99582000-99589400	Weak transcription	Right Ventricle	heart
35	chr3:99582200-99585200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:99582200-99585200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:99582200-99585200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:99582200-99585200	Strong transcription	HSMMtube	muscle
39	chr3:99582200-99585400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:99582200-99586400	Weak transcription	Psoas Muscle	Psoas
41	chr3:99582200-99587000	Weak transcription	Right Atrium	heart
42	chr3:99582400-99585200	Weak transcription	Fetal Intestine Small	intestine
43	chr3:99582400-99585200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:99582400-99587000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:99582400-99587000	Weak transcription	NHEK	skin
46	chr3:99582400-99589400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:99582600-99587000	Weak transcription	Placenta	Placenta
48	chr3:99582800-99585200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:99583000-99585400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:99583000-99587200	Enhancers	Rectal Smooth Muscle	rectum

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