Variant report

Variant	rs6499333
Chromosome Location	chr16:70701280-70701281
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70700778..70704017-chr16:70704220..70706631,3	K562	blood:
2	chr16:70700082..70702033-chr16:70779098..70781687,2	MCF-7	breast:
3	chr16:70696273..70698842-chr16:70700749..70702411,2	MCF-7	breast:
4	chr16:70695544..70698272-chr16:70698602..70701908,3	K562	blood:
5	chr16:70699407..70701314-chr16:70720329..70722044,2	MCF-7	breast:
6	chr16:70697692..70701444-chr16:70709589..70713231,3	MCF-7	breast:
7	chr16:70688760..70693483-chr16:70698297..70703877,5	K562	blood:

Variant related genes	Relation type
ENSG00000260156	Chromatin interaction
ENSG00000132613	Chromatin interaction
ENSG00000268927	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11075777	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11075778	0.84[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11075779	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.83[EUR][1000 genomes]
rs11075780	0.82[CHB][hapmap];0.85[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs11640399	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11643085	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11646834	0.83[EUR][1000 genomes]
rs11647479	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.83[MEX][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12597717	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12599324	0.81[EUR][1000 genomes]
rs12920683	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12921898	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864755	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3826272	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs4985416	0.88[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs4985557	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4985560	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.80[EUR][1000 genomes]
rs56264804	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7195572	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517391	chr16:70666410-70840490	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv457517	chr16:70666722-70840490	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv572945	chr16:70666722-70840490	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv906874	chr16:70677785-70740707	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv906875	chr16:70677785-70742536	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv906876	chr16:70677785-70757555	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv906877	chr16:70677785-70766378	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	18 gene(s)	inside rSNPs	diseases
8	nsv906878	chr16:70677785-70782922	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
9	nsv906879	chr16:70677785-70790831	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv906880	chr16:70677785-70796515	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv906882	chr16:70690989-70725815	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	nsv906883	chr16:70694000-70704974	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv572946	chr16:70694000-70740707	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
14	nsv471094	chr16:70694000-70749970	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
15	nsv906884	chr16:70696009-70725815	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
16	nsv906885	chr16:70696367-70742536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6499333	RLTPR	cis	cerebellum	SCAN
rs6499333	KLHL29	trans	cerebellum	SCAN
rs6499333	IL34	cis	parietal	SCAN
rs6499333	DKKL1	trans	cerebellum	SCAN
rs6499333	TMED6	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70688200-70701400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr16:70688200-70704800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr16:70688400-70701800	Weak transcription	Right Atrium	heart
4	chr16:70688400-70702400	Weak transcription	Psoas Muscle	Psoas
5	chr16:70688400-70715000	Weak transcription	Stomach Mucosa	stomach
6	chr16:70688600-70702400	Weak transcription	Hela-S3	cervix
7	chr16:70688600-70702400	Weak transcription	K562	blood
8	chr16:70694600-70720200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr16:70695400-70702600	Strong transcription	Brain Germinal Matrix	brain
10	chr16:70695400-70702600	Strong transcription	Thymus	Thymus
11	chr16:70695400-70702800	Strong transcription	Fetal Brain Female	brain
12	chr16:70695600-70712600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr16:70695600-70714200	Strong transcription	Placenta	Placenta
14	chr16:70695600-70714400	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr16:70695600-70714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr16:70695600-70714400	Strong transcription	Lung	lung
17	chr16:70695600-70714600	Strong transcription	Liver	Liver
18	chr16:70695800-70702600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr16:70695800-70702600	Strong transcription	HepG2	liver
20	chr16:70695800-70713800	Strong transcription	Fetal Intestine Large	intestine
21	chr16:70695800-70714200	Strong transcription	NHDF-Ad	bronchial
22	chr16:70696000-70702000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr16:70696000-70702600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr16:70696000-70707000	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr16:70696000-70714200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr16:70696000-70714200	Strong transcription	Fetal Thymus	thymus
27	chr16:70696400-70705000	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr16:70696400-70713400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr16:70696400-70714200	Strong transcription	Fetal Intestine Small	intestine
30	chr16:70696600-70702600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr16:70696600-70713400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr16:70696600-70714200	Strong transcription	Fetal Lung	lung
33	chr16:70696800-70713600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr16:70696800-70714200	Strong transcription	Osteobl	bone
35	chr16:70697000-70702600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr16:70697000-70704600	Strong transcription	Colon Smooth Muscle	Colon
37	chr16:70697200-70702400	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr16:70697200-70702600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr16:70697200-70709800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr16:70697200-70709800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr16:70697200-70713400	Strong transcription	Adipose Nuclei	Adipose
42	chr16:70697400-70702400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr16:70697400-70702400	Weak transcription	Fetal Heart	heart
44	chr16:70697400-70706000	Strong transcription	Brain Anterior Caudate	brain
45	chr16:70697400-70713400	Strong transcription	A549	lung
46	chr16:70697600-70709800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr16:70697600-70713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr16:70697600-70713600	Strong transcription	Fetal Stomach	stomach
49	chr16:70697600-70713600	Strong transcription	Ovary	ovary
50	chr16:70697600-70713800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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