Variant report

Variant	rs7757864
Chromosome Location	chr6:86381361-86381362
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86338689..86357756-chr6:86378394..86390434,115	MCF-7	breast:
2	chr6:86368977..86370570-chr6:86379098..86381596,2	MCF-7	breast:
3	chr6:86323280..86334231-chr6:86380512..86390230,24	K562	blood:

Variant related genes	Relation type
ENSG00000236016	Chromatin interaction
ENSG00000271793	Chromatin interaction
ENSG00000220563	Chromatin interaction
ENSG00000135316	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1059306	0.86[EUR][1000 genomes]
rs10806334	0.82[EUR][1000 genomes]
rs10944133	0.87[EUR][1000 genomes]
rs1173415	0.84[EUR][1000 genomes]
rs1173417	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12205013	0.82[EUR][1000 genomes]
rs12212560	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2475790	0.87[EUR][1000 genomes]
rs2475791	0.87[EUR][1000 genomes]
rs2475792	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2758840	0.80[EUR][1000 genomes]
rs2758842	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2758843	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2758844	0.82[EUR][1000 genomes]
rs2758845	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2758846	0.82[EUR][1000 genomes]
rs2758847	0.85[EUR][1000 genomes]
rs2783171	0.87[EUR][1000 genomes]
rs2842601	0.82[EUR][1000 genomes]
rs2842602	0.82[EUR][1000 genomes]
rs2842603	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2842604	0.86[EUR][1000 genomes]
rs2842607	0.86[EUR][1000 genomes]
rs2842612	0.80[EUR][1000 genomes]
rs2842614	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2842617	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3812133	0.86[EUR][1000 genomes]
rs4145082	0.80[EUR][1000 genomes]
rs6909767	0.89[EUR][1000 genomes]
rs6935918	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7742691	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7752502	0.94[EUR][1000 genomes]
rs7762321	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7771612	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7775864	0.90[EUR][1000 genomes]
rs911927	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9342041	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9344533	0.90[EUR][1000 genomes]
rs9344542	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9351065	0.87[EUR][1000 genomes]
rs9353320	0.92[EUR][1000 genomes]
rs9353327	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9359658	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9362230	0.80[EUR][1000 genomes]
rs9362233	0.87[EUR][1000 genomes]
rs9362239	0.80[EUR][1000 genomes]
rs9450302	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9450318	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
4	nsv1028293	chr6:86353958-86778912	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases
5	nsv538350	chr6:86353958-86778912	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	100 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs7757864	SNHG5	cis	Thyroid	GTEx
rs7757864	SNHG5	cis	Artery Tibial	GTEx
rs7757864	SNHG5	cis	Nerve Tibial	GTEx
rs7757864	SNHG5	cis	Muscle Skeletal	GTEx
rs7757864	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs7757864	SNHG5	cis	Adipose Subcutaneous	GTEx
rs7757864	SNHG5	cis	Stomach	GTEx
rs7757864	SNHG5	cis	Esophagus Muscularis	GTEx
rs7757864	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs7757864	SNHG5	cis	lung	GTEx
rs7757864	SNHG5	cis	Heart Left Ventricle	GTEx
rs7757864	SNHG5	cis	Whole Blood	GTEx
rs7757864	SNHG5	cis	Artery Aorta	GTEx
rs7757864	SNHG5	cis	Esophagus Mucosa	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86354600-86384200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr6:86355400-86384400	Weak transcription	Pancreas	Pancrea
3	chr6:86367800-86381800	Weak transcription	Lung	lung
4	chr6:86368200-86384800	Weak transcription	Right Ventricle	heart
5	chr6:86368600-86382600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:86368600-86384800	Weak transcription	Spleen	Spleen
7	chr6:86370200-86384400	Weak transcription	Esophagus	oesophagus
8	chr6:86370200-86384400	Weak transcription	Fetal Brain Male	brain
9	chr6:86370200-86385200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:86370400-86382600	Weak transcription	A549	lung
11	chr6:86370400-86383200	Weak transcription	Aorta	Aorta
12	chr6:86370400-86384400	Weak transcription	Psoas Muscle	Psoas
13	chr6:86370400-86385200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:86370400-86386800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:86370800-86384600	Weak transcription	HSMMtube	muscle
16	chr6:86371400-86383400	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:86373000-86384400	Weak transcription	Brain Anterior Caudate	brain
18	chr6:86373200-86381800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr6:86373600-86382000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:86374000-86385000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:86374600-86381800	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:86374600-86384400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:86374600-86385600	Weak transcription	Colonic Mucosa	Colon
24	chr6:86374800-86384800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:86375800-86381600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr6:86375800-86383400	Weak transcription	Liver	Liver
27	chr6:86375800-86384400	Weak transcription	Fetal Brain Female	brain
28	chr6:86375800-86384800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr6:86375800-86385600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:86375800-86385800	Weak transcription	Left Ventricle	heart
31	chr6:86376000-86382400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr6:86376000-86384800	Weak transcription	Brain Germinal Matrix	brain
33	chr6:86377200-86384600	Weak transcription	Ovary	ovary
34	chr6:86377400-86384400	Weak transcription	Fetal Intestine Large	intestine
35	chr6:86377600-86381400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:86377600-86384600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr6:86377800-86381600	Weak transcription	Fetal Stomach	stomach
38	chr6:86378200-86382000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:86378400-86381600	Weak transcription	Placenta	Placenta
40	chr6:86378600-86382200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:86379600-86381800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr6:86379600-86385000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:86379800-86384400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:86380000-86381800	Weak transcription	Fetal Thymus	thymus
45	chr6:86380000-86384800	Weak transcription	Primary B cells from cord blood	blood
46	chr6:86380200-86384600	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr6:86380400-86382600	Strong transcription	Fetal Intestine Small	intestine
48	chr6:86380400-86383400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:86380400-86383600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:86380400-86384400	Weak transcription	NHLF	lung

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