Variant report

Variant	rs2842601
Chromosome Location	chr6:86330133-86330134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:86323280..86334231-chr6:86380512..86390230,24	K562	blood:
2	chr6:86319220..86322208-chr6:86328498..86330402,2	MCF-7	breast:
3	chr6:86324041..86326857-chr6:86327434..86330198,2	K562	blood:
4	chr6:86324041..86327385-chr6:86327434..86331742,5	K562	blood:
5	chr6:86314714..86316790-chr6:86327729..86330292,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203875	Chromatin interaction
ENSG00000271793	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1059306	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10944133	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10944137	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs1173415	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1173417	0.83[CEU][hapmap]
rs11755642	0.82[CEU][hapmap]
rs11758508	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs12192546	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs12193904	0.81[CEU][hapmap]
rs12199873	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203963	0.83[CEU][hapmap]
rs12205013	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12212480	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs12212560	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs13207173	0.82[CEU][hapmap]
rs1335442	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs1470531	0.82[CEU][hapmap]
rs1885607	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2065114	0.86[CHB][hapmap]
rs2225754	0.82[CEU][hapmap]
rs2229523	0.85[ASN][1000 genomes]
rs2475790	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2475791	0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2475792	0.86[CEU][hapmap]
rs2484355	0.88[EUR][1000 genomes]
rs2758840	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2758842	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2758843	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs2758844	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758845	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2758846	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758847	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758848	0.83[CEU][hapmap]
rs2783171	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2842600	0.83[CEU][hapmap]
rs2842602	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842603	0.86[CEU][hapmap]
rs2842604	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2842608	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842609	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2842611	0.83[CEU][hapmap]
rs2842612	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842613	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2842614	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs2842617	0.85[EUR][1000 genomes]
rs3087978	0.82[CEU][hapmap]
rs3812133	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145082	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4235826	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4235827	0.85[ASN][1000 genomes]
rs4304137	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4348284	0.83[CEU][hapmap]
rs4351223	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs4383777	0.84[EUR][1000 genomes]
rs4419647	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4431401	0.83[CEU][hapmap]
rs4441928	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4501401	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4579322	0.84[CHB][hapmap]
rs4706240	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4707207	0.86[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs4707209	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4707211	0.83[CEU][hapmap]
rs4707217	0.86[EUR][1000 genomes]
rs6454471	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6454486	0.84[EUR][1000 genomes]
rs6454487	0.82[CEU][hapmap];0.80[TSI][hapmap]
rs6909767	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs6922	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6926049	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6935918	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs7452605	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7742201	1.00[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs7742691	0.91[CEU][hapmap]
rs7746065	0.86[CHB][hapmap]
rs7757864	0.82[EUR][1000 genomes]
rs7768065	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7770359	0.80[ASN][1000 genomes]
rs7771612	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs7775864	0.83[EUR][1000 genomes]
rs911927	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs9294337	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9342041	0.84[EUR][1000 genomes]
rs9342046	0.82[EUR][1000 genomes]
rs9344532	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9344533	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs9344542	0.87[CEU][hapmap]
rs9351065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9353318	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9353320	0.84[EUR][1000 genomes]
rs9353327	0.87[CEU][hapmap]
rs9359658	0.82[EUR][1000 genomes]
rs9362230	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9362233	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9362239	0.85[EUR][1000 genomes]
rs9444349	0.85[ASN][1000 genomes]
rs9444352	0.83[CEU][hapmap]
rs9450284	0.82[CEU][hapmap]
rs9450285	0.83[CEU][hapmap]
rs9450290	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9450302	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs9450318	0.85[EUR][1000 genomes]
rs9450319	0.84[EUR][1000 genomes]
rs9647601	0.82[CEU][hapmap]

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	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
5	nsv5383	chr6:86303223-86348023	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs2842601	SNHG5	cis	Artery Tibial	GTEx
rs2842601	SNHG5	cis	lung	GTEx
rs2842601	SNHG5	cis	Whole Blood	GTEx
rs2842601	SNHG5	cis	Nerve Tibial	GTEx
rs2842601	SNHG5	cis	Esophagus Mucosa	GTEx
rs2842601	SNHG5	cis	Heart Left Ventricle	GTEx
rs2842601	SNHG5	Cis_1M	lymphoblastoid	RTeQTL
rs2842601	SNHG5	cis	Esophagus Muscularis	GTEx
rs2842601	SNHG5	cis	Skin Sun Exposed Lower leg	GTEx
rs2842601	SNHG5	cis	Thyroid	GTEx
rs2842601	SNHG5	cis	multi-tissue	Pritchard
rs2842601	SNHG5	cis	Muscle Skeletal	GTEx
rs2842601	SNHG5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86304600-86331400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:86305800-86336200	Weak transcription	Fetal Heart	heart
3	chr6:86307600-86331000	Strong transcription	HSMM	muscle
4	chr6:86313400-86349000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr6:86313600-86338400	Strong transcription	GM12878-XiMat	blood
6	chr6:86313800-86340200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:86314200-86338200	Strong transcription	Dnd41	blood
8	chr6:86314200-86341200	Strong transcription	HMEC	breast
9	chr6:86314600-86334600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr6:86314800-86348600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:86315000-86347800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr6:86315200-86338200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:86315400-86338200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:86315400-86338200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:86315400-86347400	Strong transcription	HUVEC	blood vessel
16	chr6:86315600-86330200	Strong transcription	NH-A	brain
17	chr6:86315600-86331000	Strong transcription	NHDF-Ad	bronchial
18	chr6:86315800-86330400	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr6:86316000-86348600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr6:86316200-86339200	Strong transcription	Primary B cells from cord blood	blood
21	chr6:86316200-86347800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:86316200-86348600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr6:86316200-86348600	Strong transcription	Placenta	Placenta
24	chr6:86316200-86348800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr6:86316400-86348200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:86316400-86348400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr6:86316400-86349200	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr6:86316400-86350600	Strong transcription	Fetal Thymus	thymus
29	chr6:86317000-86337400	Strong transcription	Primary T cells from cord blood	blood
30	chr6:86317000-86340400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:86317000-86349000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:86317400-86338800	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr6:86317400-86349000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr6:86317600-86349800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr6:86317800-86337600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr6:86317800-86348200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr6:86318600-86348800	Strong transcription	Primary B cells from peripheral blood	blood
38	chr6:86318800-86347200	Strong transcription	Fetal Brain Female	brain
39	chr6:86319000-86333800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:86319000-86350000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr6:86319200-86330200	Strong transcription	NHLF	lung
42	chr6:86319200-86333600	Strong transcription	Adipose Nuclei	Adipose
43	chr6:86319400-86348600	Strong transcription	K562	blood
44	chr6:86319600-86342400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr6:86319600-86348200	Strong transcription	NHEK	skin
46	chr6:86319600-86348800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:86319600-86350000	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr6:86320000-86344200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:86320000-86348600	Strong transcription	Liver	Liver
50	chr6:86320200-86333600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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