Variant report

Variant	rs6935918
Chromosome Location	chr6:86283575-86283576
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86280113..86284148-chr6:86385938..86389543,4	K562	blood:
2	chr6:86281475..86283897-chr6:86288113..86290341,2	K562	blood:
3	chr6:86281941..86283670-chr6:86301827..86303661,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1059306	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs1059307	0.87[CEU][hapmap]
rs10944128	0.83[CEU][hapmap]
rs1173417	0.91[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.87[EUR][1000 genomes]
rs1173418	0.84[CEU][hapmap]
rs12199873	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs12203963	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs12205013	0.84[EUR][1000 genomes]
rs12212560	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2475790	0.91[CEU][hapmap]
rs2475792	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs2758840	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs2758842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2758844	0.84[EUR][1000 genomes]
rs2758845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2758846	0.86[CEU][hapmap]
rs2758847	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs2758848	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2783171	0.91[CEU][hapmap]
rs2842600	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2842601	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2842602	0.84[EUR][1000 genomes]
rs2842603	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2842604	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842607	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs2842608	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2842609	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2842611	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs2842612	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs2842613	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2842614	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842617	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087978	0.91[CEU][hapmap]
rs3812133	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs4304137	0.91[CEU][hapmap]
rs4348284	0.91[CEU][hapmap]
rs4351223	0.91[CEU][hapmap]
rs4373337	0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4419647	0.83[EUR][1000 genomes]
rs4431401	0.91[CEU][hapmap]
rs4441928	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4593336	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4706240	0.85[EUR][1000 genomes]
rs4707211	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs6454471	0.91[CEU][hapmap]
rs6454472	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs6454473	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6909767	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6922	0.91[CEU][hapmap]
rs7452605	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7742201	0.90[CEU][hapmap]
rs7742691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7752502	0.88[EUR][1000 genomes]
rs7757864	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7762321	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7766485	0.87[CEU][hapmap];0.83[CHB][hapmap]
rs7768065	0.86[EUR][1000 genomes]
rs7771612	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7775864	0.83[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs911927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9294337	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs9342041	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9344532	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs9344533	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9344542	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs9351065	0.91[CEU][hapmap]
rs9353318	0.86[CEU][hapmap];0.84[EUR][1000 genomes]
rs9353320	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9353327	0.95[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes]
rs9359658	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9362230	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs9444352	0.91[CEU][hapmap];0.83[CHB][hapmap]
rs9450282	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9450285	0.91[CEU][hapmap]
rs9450287	0.90[ASN][1000 genomes]
rs9450288	0.83[CHB][hapmap]
rs9450290	0.84[EUR][1000 genomes]
rs9450302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	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
6	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs6935918	SNHG5	cis	Esophagus Muscularis	GTEx
rs6935918	SNHG5	cis	Muscle Skeletal	GTEx
rs6935918	SNHG5	cis	Nerve Tibial	GTEx
rs6935918	C6orf160	cis	lesional skin	skin_eQTL
rs6935918	SNHG5	cis	Artery Tibial	GTEx
rs6935918	SNHG5	cis	lung	GTEx
rs6935918	C6orf160	cis	normal skin	skin_eQTL
rs6935918	SNHG5	cis	Thyroid	GTEx
rs6935918	SNHG5	cis	Whole Blood	GTEx
rs6935918	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs6935918	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs6935918	SNHG5	cis	multi-tissue	Pritchard
rs6935918	SNHG5	cis	Esophagus Mucosa	GTEx
rs6935918	SNHG5	cis	Heart Left Ventricle	GTEx
rs6935918	C6orf160	cis	uninvolved skin	skin_eQTL
rs6935918	SNHG5	cis	Adipose Subcutaneous	GTEx
rs6935918	SNHG5	cis	Artery Aorta	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86208800-86284600	Weak transcription	Small Intestine	intestine
2	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
3	chr6:86221800-86285800	Weak transcription	Fetal Brain Male	brain
4	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:86223400-86285000	Weak transcription	Brain Substantia Nigra	brain
6	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
7	chr6:86231200-86285000	Weak transcription	Hela-S3	cervix
8	chr6:86233800-86289200	Weak transcription	Spleen	Spleen
9	chr6:86241400-86283600	Weak transcription	Fetal Kidney	kidney
10	chr6:86243200-86285200	Weak transcription	Psoas Muscle	Psoas
11	chr6:86243200-86286000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
13	chr6:86243600-86285000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:86243600-86285800	Weak transcription	Fetal Brain Female	brain
15	chr6:86243600-86286200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr6:86243800-86284800	Weak transcription	Brain Angular Gyrus	brain
17	chr6:86244200-86286000	Weak transcription	Right Ventricle	heart
18	chr6:86244200-86289200	Weak transcription	Gastric	stomach
19	chr6:86250200-86284800	Weak transcription	Aorta	Aorta
20	chr6:86252800-86284400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:86252800-86289600	Weak transcription	Esophagus	oesophagus
22	chr6:86253400-86286000	Weak transcription	Brain Germinal Matrix	brain
23	chr6:86254800-86287800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr6:86257600-86285200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:86258000-86284800	Weak transcription	Fetal Heart	heart
26	chr6:86258000-86286000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr6:86258400-86284400	Weak transcription	A549	lung
28	chr6:86263000-86284600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:86263000-86284800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:86263000-86289400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr6:86263000-86289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:86265600-86288200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:86265600-86289800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr6:86266400-86290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:86270400-86286200	Weak transcription	Brain Anterior Caudate	brain
36	chr6:86272000-86284800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr6:86272000-86290200	Weak transcription	Fetal Muscle Leg	muscle
38	chr6:86272200-86286200	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:86273400-86288000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr6:86275200-86286400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr6:86276000-86284800	Weak transcription	Brain Hippocampus Middle	brain
42	chr6:86276000-86285800	Weak transcription	Dnd41	blood
43	chr6:86277600-86289200	Weak transcription	Lung	lung
44	chr6:86278200-86302600	Weak transcription	Ovary	ovary
45	chr6:86278400-86284800	Weak transcription	Fetal Lung	lung
46	chr6:86278400-86284800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:86278400-86291400	Weak transcription	Adipose Nuclei	Adipose
48	chr6:86279200-86286200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:86279200-86289200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:86279400-86284600	Weak transcription	NH-A	brain

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