Variant report

Variant	rs4985557
Chromosome Location	chr16:70704974-70704975
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:70704267..70706050-chr16:70717985..70719949,2	MCF-7	breast:
2	chr16:70700778..70704017-chr16:70704220..70706631,3	K562	blood:
3	chr16:70703850..70706247-chr16:70735267..70737927,2	MCF-7	breast:
4	chr16:70704478..70706991-chr16:70709416..70711257,2	K562	blood:

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11075777	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11075778	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11075779	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11075780	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11639579	1.00[MKK][hapmap]
rs11640399	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11643085	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11646834	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11647479	0.96[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11649476	0.84[ASW][hapmap];0.80[GIH][hapmap];0.83[MEX][hapmap]
rs12597717	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12599324	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12920683	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12921898	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1551526	1.00[ASW][hapmap]
rs2864755	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35874206	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3826272	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];0.81[EUR][1000 genomes]
rs4985416	0.92[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4985560	0.92[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.82[EUR][1000 genomes]
rs56264804	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6499333	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]
rs7195572	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4985557	TMED6	cis	cerebellum	SCAN
rs4985557	DKKL1	trans	cerebellum	SCAN
rs4985557	IL34	cis	parietal	SCAN
rs4985557	RLTPR	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:70688400-70715000	Weak transcription	Stomach Mucosa	stomach
2	chr16:70694600-70720200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:70695600-70712600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr16:70695600-70714200	Strong transcription	Placenta	Placenta
5	chr16:70695600-70714400	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr16:70695600-70714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr16:70695600-70714400	Strong transcription	Lung	lung
8	chr16:70695600-70714600	Strong transcription	Liver	Liver
9	chr16:70695800-70713800	Strong transcription	Fetal Intestine Large	intestine
10	chr16:70695800-70714200	Strong transcription	NHDF-Ad	bronchial
11	chr16:70696000-70707000	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr16:70696000-70714200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr16:70696000-70714200	Strong transcription	Fetal Thymus	thymus
14	chr16:70696400-70705000	Strong transcription	Brain Inferior Temporal Lobe	brain
15	chr16:70696400-70713400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr16:70696400-70714200	Strong transcription	Fetal Intestine Small	intestine
17	chr16:70696600-70713400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr16:70696600-70714200	Strong transcription	Fetal Lung	lung
19	chr16:70696800-70713600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr16:70696800-70714200	Strong transcription	Osteobl	bone
21	chr16:70697200-70709800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr16:70697200-70709800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr16:70697200-70713400	Strong transcription	Adipose Nuclei	Adipose
24	chr16:70697400-70706000	Strong transcription	Brain Anterior Caudate	brain
25	chr16:70697400-70713400	Strong transcription	A549	lung
26	chr16:70697600-70709800	Strong transcription	Stomach Smooth Muscle	stomach
27	chr16:70697600-70713000	Strong transcription	Duodenum Smooth Muscle	Duodenum
28	chr16:70697600-70713600	Strong transcription	Fetal Stomach	stomach
29	chr16:70697600-70713600	Strong transcription	Ovary	ovary
30	chr16:70697600-70713800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr16:70697600-70714200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:70698000-70712200	Strong transcription	Cortex derived primary cultured neurospheres	brain
33	chr16:70698000-70713200	Strong transcription	HSMMtube	muscle
34	chr16:70698000-70714400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr16:70698600-70708200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr16:70698800-70705200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr16:70698800-70711600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr16:70698800-70713400	Strong transcription	NHLF	lung
39	chr16:70699000-70710200	Strong transcription	Fetal Muscle Leg	muscle
40	chr16:70699200-70711200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr16:70699600-70713400	Strong transcription	HSMM	muscle
42	chr16:70700000-70707200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr16:70700000-70708200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr16:70700200-70708200	Strong transcription	Fetal Muscle Trunk	muscle
45	chr16:70700200-70708200	Weak transcription	Gastric	stomach
46	chr16:70700400-70706800	Weak transcription	Pancreas	Pancrea
47	chr16:70700400-70711000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr16:70700400-70718800	Weak transcription	Small Intestine	intestine
49	chr16:70700600-70711400	Weak transcription	Colonic Mucosa	Colon
50	chr16:70701000-70705600	Weak transcription	H9 Cell Line	embryonic stem cell

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