Variant report

Variant	rs6496969
Chromosome Location	chr15:93196817-93196818
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93145840..93149737-chr15:93196292..93199149,3	MCF-7	breast:
2	chr15:93196488..93198404-chr17:67442282..67443797,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271763	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12443091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496712	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16974307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254142	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs2453901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285754	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs285755	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs285757	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs285758	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs285766	0.82[EUR][1000 genomes]
rs285772	0.92[EUR][1000 genomes]
rs366789	0.84[EUR][1000 genomes]
rs373481	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs406032	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413450	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434826	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs503112	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178546	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6496969	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93171000-93197400	Weak transcription	Primary T cells from cord blood	blood
2	chr15:93182000-93197800	Weak transcription	Small Intestine	intestine
3	chr15:93182600-93197200	Weak transcription	Fetal Kidney	kidney
4	chr15:93183200-93198400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:93189000-93197000	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:93189400-93197000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:93189400-93197000	Weak transcription	Esophagus	oesophagus
8	chr15:93190600-93197000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:93191000-93197400	Weak transcription	HSMMtube	muscle
10	chr15:93192000-93197400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:93193800-93199000	Enhancers	Fetal Heart	heart
12	chr15:93194000-93197200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:93194000-93197400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:93194200-93197000	Weak transcription	Ovary	ovary
15	chr15:93194200-93197400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:93194200-93198200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:93194400-93197400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:93194400-93198400	Weak transcription	Brain Anterior Caudate	brain
19	chr15:93194600-93197400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr15:93194600-93197600	Weak transcription	Fetal Brain Female	brain
21	chr15:93194600-93198400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:93195000-93197000	Active TSS	GM12878-XiMat	blood
23	chr15:93195000-93197600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:93195200-93197200	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr15:93195200-93197200	Enhancers	Placenta	Placenta
26	chr15:93195200-93199600	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr15:93195400-93197000	Enhancers	Stomach Mucosa	stomach
28	chr15:93195400-93197200	Strong transcription	Fetal Stomach	stomach
29	chr15:93195400-93197200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr15:93195400-93197600	Flanking Active TSS	Pancreas	Pancrea
31	chr15:93195400-93197600	Enhancers	Right Ventricle	heart
32	chr15:93195600-93197200	Genic enhancers	Fetal Lung	lung
33	chr15:93195600-93197600	Enhancers	Fetal Intestine Large	intestine
34	chr15:93195600-93197600	Genic enhancers	Fetal Muscle Leg	muscle
35	chr15:93195600-93198000	Enhancers	Right Atrium	heart
36	chr15:93195800-93197200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr15:93195800-93197400	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:93195800-93197600	Enhancers	Brain Angular Gyrus	brain
39	chr15:93195800-93198400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:93196000-93197200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:93196000-93197400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr15:93196000-93197400	Enhancers	Duodenum Mucosa	Duodenum
43	chr15:93196200-93197200	Enhancers	Gastric	stomach
44	chr15:93196200-93197200	Enhancers	HUVEC	blood vessel
45	chr15:93196200-93198000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr15:93196200-93198200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr15:93196400-93197000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:93196400-93197200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr15:93196400-93197200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr15:93196400-93197200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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