Variant report

Variant	rs6787184
Chromosome Location	chr3:99653408-99653409
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	chr3:99652546..99654648-chr3:99721251..99724198,2	MCF-7	breast:
2	chr3:99651699..99654533-chr3:99662163..99665139,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL8A1-5	chr3:99652069-99654106	NONHSAT090856

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs16841712	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs17313676	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17314245	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17314280	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17314998	1.00[ASW][hapmap]
rs17392822	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17393080	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs17778804	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs2035400	1.00[YRI][hapmap]
rs41444055	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs41477051	1.00[AFR][1000 genomes]
rs6762809	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6762871	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6764470	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6765822	1.00[AFR][1000 genomes]
rs6772519	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6778756	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6781780	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap]
rs6784150	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6788807	1.00[YRI][hapmap]
rs6789840	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6790187	0.89[AFR][1000 genomes]
rs6791426	1.00[ASW][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6794365	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6801514	1.00[YRI][hapmap]
rs6805703	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6805834	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs6807137	1.00[YRI][hapmap]
rs6807615	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6808420	1.00[YRI][hapmap]
rs7611313	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7619738	1.00[YRI][hapmap]
rs7626214	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs7626310	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7639304	0.89[AFR][1000 genomes]
rs766777	0.89[AFR][1000 genomes]
rs768527	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9756455	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99640400-99656000	Weak transcription	GM12878-XiMat	blood
2	chr3:99640400-99656600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:99640400-99656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr3:99641400-99654200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr3:99642200-99654000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:99644800-99653800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr3:99644800-99663200	Weak transcription	Esophagus	oesophagus
8	chr3:99645200-99653800	Weak transcription	NHLF	lung
9	chr3:99645200-99654200	Weak transcription	Small Intestine	intestine
10	chr3:99645200-99656800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:99645400-99653800	Weak transcription	NHDF-Ad	bronchial
12	chr3:99646000-99656400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:99648600-99654000	Weak transcription	Ovary	ovary
14	chr3:99648600-99656400	Weak transcription	Fetal Brain Male	brain
15	chr3:99648800-99654200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:99648800-99656800	Weak transcription	Fetal Heart	heart
17	chr3:99648800-99656800	Weak transcription	Psoas Muscle	Psoas
18	chr3:99648800-99663200	Weak transcription	Gastric	stomach
19	chr3:99648800-99664000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:99649000-99653800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:99649000-99656200	Weak transcription	NH-A	brain
22	chr3:99649200-99653800	Weak transcription	Osteobl	bone
23	chr3:99649400-99653800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:99649400-99653800	Weak transcription	Fetal Lung	lung
25	chr3:99649400-99654200	Weak transcription	Brain Anterior Caudate	brain
26	chr3:99649400-99656200	Weak transcription	HSMM	muscle
27	chr3:99649400-99656400	Weak transcription	Brain Angular Gyrus	brain
28	chr3:99649600-99653600	Weak transcription	Brain Substantia Nigra	brain
29	chr3:99649600-99653800	Weak transcription	Adipose Nuclei	Adipose
30	chr3:99649600-99653800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:99649600-99654000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:99649600-99654200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:99649600-99654200	Weak transcription	Stomach Mucosa	stomach
34	chr3:99649600-99656200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:99649600-99662800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:99649800-99653600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:99649800-99653600	Weak transcription	NHEK	skin
38	chr3:99649800-99653800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:99649800-99653800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:99649800-99653800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:99649800-99653800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:99649800-99654200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:99649800-99654200	Weak transcription	Aorta	Aorta
44	chr3:99649800-99654200	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:99649800-99654200	Weak transcription	Left Ventricle	heart
46	chr3:99649800-99654200	Weak transcription	Right Atrium	heart
47	chr3:99649800-99654200	Weak transcription	Right Ventricle	heart
48	chr3:99650000-99653600	Weak transcription	Fetal Intestine Small	intestine
49	chr3:99650000-99654200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr3:99650000-99654200	Weak transcription	Fetal Stomach	stomach

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