Variant report

Variant	rs178734
Chromosome Location	chr7:127714418-127714419
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127705316..127708471-chr7:127714024..127716171,3	MCF-7	breast:
2	chr7:127710993..127713528-chr7:127713751..127716663,2	K562	blood:
3	chr7:127712887..127715958-chr7:127718524..127721736,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1193336	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs124756	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs1345509	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178733	0.80[CHB][hapmap]
rs2241291	0.88[JPT][hapmap]
rs225241	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322779	0.86[ASN][1000 genomes]
rs322813	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs322819	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs322820	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs322821	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs322823	0.90[CHB][hapmap];0.88[JPT][hapmap]
rs322825	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs322826	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes]
rs322827	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322828	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322831	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322832	0.97[EUR][1000 genomes]
rs322833	0.97[EUR][1000 genomes]
rs322834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs322835	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322836	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322838	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs322840	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs35774036	0.84[ASN][1000 genomes]
rs3757753	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3757755	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3757760	0.88[JPT][hapmap]
rs3757763	0.88[JPT][hapmap]
rs3779523	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs3779526	0.85[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3808055	0.82[EUR][1000 genomes]
rs3808056	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3808061	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3808077	0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs3808088	0.81[JPT][hapmap]
rs3823995	0.85[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.96[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6944446	0.80[CHB][hapmap]
rs6973092	0.85[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1022385	chr7:127246656-127971194	Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv539120	chr7:127246656-127971194	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv1016143	chr7:127251359-127726762	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs178734	ATP6V1F	cis	parietal	SCAN
rs178734	TMEM209	cis	cerebellum	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127669400-127726600	Weak transcription	Hela-S3	cervix
2	chr7:127669600-127718200	Weak transcription	A549	lung
3	chr7:127673800-127715400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:127681000-127716200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr7:127681200-127718200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr7:127681600-127714600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr7:127689400-127717000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr7:127692800-127724200	Weak transcription	Right Atrium	heart
9	chr7:127693200-127718400	Weak transcription	HMEC	breast
10	chr7:127693400-127716600	Weak transcription	Colonic Mucosa	Colon
11	chr7:127693400-127717200	Weak transcription	Small Intestine	intestine
12	chr7:127694400-127716800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr7:127694800-127717200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:127695200-127718000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr7:127697200-127714800	Weak transcription	HUVEC	blood vessel
16	chr7:127698400-127714600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:127699800-127714600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr7:127700400-127714600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:127700400-127714600	Weak transcription	Left Ventricle	heart
20	chr7:127700400-127714800	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr7:127700400-127715400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr7:127700400-127715400	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr7:127701600-127724600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr7:127702200-127714800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:127702800-127727800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr7:127703200-127715600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:127703400-127715600	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:127703400-127715600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr7:127703400-127715800	Weak transcription	NH-A	brain
30	chr7:127703600-127716600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr7:127703600-127716800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr7:127704400-127716800	Weak transcription	Ovary	ovary
33	chr7:127706600-127716000	Weak transcription	Fetal Lung	lung
34	chr7:127706800-127714600	Weak transcription	Primary B cells from cord blood	blood
35	chr7:127706800-127715400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr7:127707200-127714600	Weak transcription	Brain Anterior Caudate	brain
37	chr7:127707600-127716000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr7:127707600-127716600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr7:127707800-127742200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:127708000-127715400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr7:127708000-127716600	Weak transcription	HSMM	muscle
42	chr7:127708200-127716800	Weak transcription	Brain Substantia Nigra	brain
43	chr7:127709200-127714600	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr7:127709200-127715800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr7:127709800-127718400	Weak transcription	Colon Smooth Muscle	Colon
46	chr7:127709800-127724600	Weak transcription	NHDF-Ad	bronchial
47	chr7:127710400-127714600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:127710400-127715800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr7:127710400-127720200	Strong transcription	GM12878-XiMat	blood
50	chr7:127710600-127717200	Weak transcription	HSMMtube	muscle

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