Variant report

Variant	rs17629180
Chromosome Location	chr6:34285609-34285610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:34283435..34288525-chr6:34290742..34294904,6	K562	blood:
2	chr6:34214953..34217235-chr6:34283214..34286512,3	K562	blood:
3	chr6:34260937..34262929-chr6:34283836..34285697,2	MCF-7	breast:
4	chr6:34285140..34288176-chr6:34300410..34302551,3	MCF-7	breast:
5	chr6:34284086..34287812-chr6:34358809..34361485,3	K562	blood:

Variant related genes	Relation type
ENSG00000272325	Chromatin interaction
ENSG00000186577	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10484267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484268	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1057691	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1060308	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10648	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1127084	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13466	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883137	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16883475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16883896	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16888452	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17628798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17628946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17629270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1994923	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs206922	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3798554	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3798557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3798558	1.00[YRI][hapmap]
rs41269032	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269034	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41269036	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41269038	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4713771	0.87[EUR][1000 genomes]
rs55674397	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55684754	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55694290	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55763242	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55779010	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55798596	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55812200	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55833185	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55863933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55864834	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56033036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56039915	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56107559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56188036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56274913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56309550	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56323997	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56330729	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59832183	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62399870	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911272	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7738665	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7741127	0.80[AMR][1000 genomes]
rs7760373	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770443	1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs875274	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9368811	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	esv1798756	chr6:34203406-34319041	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv1798835	chr6:34204183-34319041	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv1792088	chr6:34204285-34318837	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	esv1793127	chr6:34204285-34319041	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
5	esv1794528	chr6:34267024-34308816	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17629180	LEMD2	cis	brain	seeQTL
rs17629180	NUDT3	cis	parietal	SCAN
rs17629180	NUP210	trans	brain	seeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34261800-34330800	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:34262000-34286600	Weak transcription	Gastric	stomach
3	chr6:34262000-34289000	Weak transcription	Hela-S3	cervix
4	chr6:34262000-34292800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:34262200-34295400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr6:34262200-34301200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr6:34262800-34290800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:34263800-34288400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr6:34264000-34299000	Weak transcription	Dnd41	blood
10	chr6:34269600-34286800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:34272600-34288200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:34274400-34306400	Weak transcription	Brain Germinal Matrix	brain
13	chr6:34274400-34309000	Weak transcription	NHDF-Ad	bronchial
14	chr6:34275200-34285800	Weak transcription	Fetal Stomach	stomach
15	chr6:34275200-34298000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr6:34275400-34286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:34275400-34289400	Weak transcription	HUVEC	blood vessel
18	chr6:34275800-34299600	Weak transcription	Lung	lung
19	chr6:34276200-34286800	Weak transcription	Ovary	ovary
20	chr6:34276400-34287000	Weak transcription	HepG2	liver
21	chr6:34276800-34286200	Weak transcription	Brain Substantia Nigra	brain
22	chr6:34280800-34295600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:34281400-34288200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr6:34282400-34287200	Enhancers	Primary hematopoietic stem cells	blood
25	chr6:34282600-34285800	Enhancers	Brain Hippocampus Middle	brain
26	chr6:34282600-34287600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr6:34282800-34286000	Flanking Active TSS	GM12878-XiMat	blood
28	chr6:34283600-34285800	Enhancers	Fetal Kidney	kidney
29	chr6:34283600-34286000	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr6:34283600-34286600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:34283800-34285800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:34283800-34287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr6:34284000-34285800	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr6:34284000-34287000	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr6:34284000-34287000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr6:34284000-34287200	Enhancers	Primary B cells from cord blood	blood
37	chr6:34284000-34287400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:34284000-34287800	Enhancers	Primary B cells from peripheral blood	blood
39	chr6:34284000-34288000	Enhancers	Fetal Heart	heart
40	chr6:34284000-34301600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:34284000-34308200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr6:34284200-34285800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:34284200-34286400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr6:34284200-34286600	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr6:34284200-34287000	Enhancers	Brain Anterior Caudate	brain
46	chr6:34284200-34287200	Enhancers	Colon Smooth Muscle	Colon
47	chr6:34284200-34287400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr6:34284400-34286400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr6:34284400-34287000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:34284400-34287200	Enhancers	Adipose Nuclei	Adipose

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