Variant report

Variant	rs10305525
Chromosome Location	chr6:39056150-39056151
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:39054886..39057587-chr6:39057914..39060553,2	MCF-7	breast:
2	chr6:38997318..38997990-chr6:39055855..39056407,2	MCF-7	breast:
3	chr6:39055895..39057214-chr6:39125035..39125985,4	MCF-7	breast:
4	chr6:39055835..39056584-chr6:39271011..39271689,3	K562	blood:
5	chr6:39055500..39058719-chr6:39195179..39198658,3	K562	blood:
6	chr6:38940723..38941491-chr6:39055376..39056317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164626	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10305479	0.89[CEU][hapmap]
rs10305516	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1076734	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs1077680	0.90[CEU][hapmap]
rs12665144	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs2268633	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2268634	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2268635	1.00[CEU][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2268636	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2268645	0.91[CEU][hapmap];0.83[TSI][hapmap]
rs2300612	0.83[CEU][hapmap];0.88[GIH][hapmap]
rs3765468	0.83[CEU][hapmap]
rs60678751	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs742761	1.00[CEU][hapmap]
rs761387	0.83[CEU][hapmap]

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	nsv1028088	chr6:38821047-39163549	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv538205	chr6:38821047-39163549	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv528286	chr6:39019503-39060478	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1031922	chr6:39034484-39060762	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv462919	chr6:39050384-39062990	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv602963	chr6:39050384-39062990	Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10305525	C6orf64	cis	parietal	SCAN
rs10305525	C6orf64	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:39021200-39072000	Weak transcription	Gastric	stomach
2	chr6:39024200-39057800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:39027400-39073000	Weak transcription	Pancreas	Pancrea
4	chr6:39043400-39082000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:39052600-39056200	Enhancers	Stomach Smooth Muscle	stomach
6	chr6:39052600-39060400	Enhancers	Fetal Heart	heart
7	chr6:39053000-39072400	Weak transcription	Brain Germinal Matrix	brain
8	chr6:39053400-39057200	Weak transcription	Lung	lung
9	chr6:39053400-39059600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr6:39053800-39058400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr6:39053800-39058600	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr6:39054000-39057800	Enhancers	Psoas Muscle	Psoas
13	chr6:39054200-39056600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:39054200-39057800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:39054400-39056600	Weak transcription	Right Atrium	heart
16	chr6:39054800-39056600	Weak transcription	Left Ventricle	heart
17	chr6:39054800-39057600	Enhancers	Fetal Muscle Leg	muscle
18	chr6:39055000-39056400	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr6:39055000-39056600	Weak transcription	Right Ventricle	heart
20	chr6:39055200-39056800	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr6:39055200-39057400	Enhancers	Fetal Lung	lung
22	chr6:39055200-39069800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:39055400-39057000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
24	chr6:39055400-39057400	Enhancers	Fetal Stomach	stomach
25	chr6:39055600-39056800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:39055600-39057000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr6:39055600-39057200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:39055600-39057600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr6:39055600-39060800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr6:39055800-39056200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr6:39055800-39056200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr6:39055800-39056800	Enhancers	Colon Smooth Muscle	Colon
33	chr6:39055800-39057200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr6:39056000-39056800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:39056000-39056800	Enhancers	Fetal Muscle Trunk	muscle
36	chr6:39056000-39057000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:39056000-39057000	Enhancers	Rectal Smooth Muscle	rectum

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