Variant report

Variant	rs6807615
Chromosome Location	chr3:99646904-99646905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99644955..99646992-chr3:99649080..99650758,2	MCF-7	breast:
2	chr3:99638906..99644679-chr3:99646570..99651799,7	K562	blood:
3	chr3:99639208..99643794-chr3:99646040..99649673,4	MCF-7	breast:

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

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

rs_ID	r²[population]
rs15890	1.00[AMR][1000 genomes]
rs16841712	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs17313676	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17314245	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314280	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17314977	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17314998	1.00[ASW][hapmap]
rs17338576	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17392822	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs17393080	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17397949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17778707	1.00[AMR][1000 genomes]
rs17778804	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17779605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2035400	1.00[GIH][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36005744	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41444055	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs41477051	0.89[AFR][1000 genomes]
rs6762809	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6762871	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6764470	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6765822	0.89[AFR][1000 genomes]
rs6772519	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6778756	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6781780	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs6784150	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6787184	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6788807	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6789840	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6790187	1.00[EUR][1000 genomes]
rs6791426	1.00[ASW][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6794130	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6794365	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6801514	1.00[YRI][hapmap]
rs6803576	1.00[AMR][1000 genomes]
rs6805703	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6805834	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs6807137	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs6808420	1.00[YRI][hapmap]
rs7611313	1.00[ASW][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7612083	1.00[YRI][hapmap]
rs7612089	1.00[YRI][hapmap]
rs7619738	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7626214	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs7626310	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7628458	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7646221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648943	1.00[EUR][1000 genomes]
rs766777	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs768527	1.00[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9756455	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

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:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99634400-99647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr3:99640000-99648400	Weak transcription	HSMMtube	muscle
4	chr3:99640200-99648400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:99640200-99648400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:99640400-99647000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:99640400-99648400	Weak transcription	Gastric	stomach
8	chr3:99640400-99648600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:99640400-99656000	Weak transcription	GM12878-XiMat	blood
10	chr3:99640400-99656600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:99640400-99656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:99641000-99648200	Weak transcription	Psoas Muscle	Psoas
13	chr3:99641200-99648400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr3:99641400-99654200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:99642200-99647000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:99642200-99654000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr3:99644000-99649800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:99644400-99647000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr3:99644400-99648400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:99644400-99648400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:99644800-99647200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:99644800-99648000	Weak transcription	Left Ventricle	heart
23	chr3:99644800-99648000	Weak transcription	Right Ventricle	heart
24	chr3:99644800-99648200	Weak transcription	Brain Anterior Caudate	brain
25	chr3:99644800-99648400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr3:99644800-99648400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:99644800-99648400	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:99644800-99648400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr3:99644800-99648400	Weak transcription	Brain Substantia Nigra	brain
30	chr3:99644800-99648400	Weak transcription	A549	lung
31	chr3:99644800-99648600	Weak transcription	Lung	lung
32	chr3:99644800-99648800	Weak transcription	Brain Germinal Matrix	brain
33	chr3:99644800-99649600	Weak transcription	Pancreas	Pancrea
34	chr3:99644800-99653800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:99644800-99663200	Weak transcription	Esophagus	oesophagus
36	chr3:99645000-99647000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:99645000-99647400	Weak transcription	Fetal Heart	heart
38	chr3:99645000-99648000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:99645000-99648400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:99645000-99648400	Weak transcription	HSMM	muscle
41	chr3:99645200-99648200	Weak transcription	HMEC	breast
42	chr3:99645200-99648200	Weak transcription	Osteobl	bone
43	chr3:99645200-99648400	Weak transcription	Aorta	Aorta
44	chr3:99645200-99648400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr3:99645200-99648400	Weak transcription	Fetal Lung	lung
46	chr3:99645200-99648400	Weak transcription	NH-A	brain
47	chr3:99645200-99648600	Weak transcription	Fetal Intestine Small	intestine
48	chr3:99645200-99653800	Weak transcription	NHLF	lung
49	chr3:99645200-99654200	Weak transcription	Small Intestine	intestine
50	chr3:99645200-99656800	Weak transcription	Rectal Mucosa Donor 29	rectum

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