Variant report

Variant	rs12597171
Chromosome Location	chr16:82200119-82200120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:82199046-82200215	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr16:82199140-82201949	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:82192311..82195081-chr16:82198371..82200683,2	K562	blood:
2	chr16:82199846..82201653-chr16:82203599..82206559,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261029	TF binding region
ENSG00000261029	Chromatin interaction
ENSG00000135698	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10514532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[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]
rs1134847	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11645286	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11859473	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11859599	0.83[CEU][hapmap]
rs11866709	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11866711	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12102917	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12595971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12597010	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12597534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][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]
rs12599946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12599988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303261	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303262	0.84[TSI][hapmap]
rs2303264	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303265	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2911423	0.83[CEU][hapmap]
rs2911425	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2911429	0.94[EUR][1000 genomes]
rs2967349	0.82[CEU][hapmap]
rs2967355	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs2967359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967361	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967363	1.00[ASN][1000 genomes]
rs2967375	0.91[EUR][1000 genomes]
rs35865749	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4889479	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62044258	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62044259	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045961	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62045964	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67612167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67661146	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7192444	0.83[CEU][hapmap]
rs7194734	0.80[EUR][1000 genomes]
rs7200628	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7202258	0.83[CEU][hapmap];0.84[TSI][hapmap]
rs7203990	0.81[TSI][hapmap]
rs7205534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7206093	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72628279	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532598	chr16:82034475-82738733	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv532599	chr16:82074439-82926863	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
3	nsv573367	chr16:82140561-83040846	Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv457579	chr16:82150293-82216622	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv573368	chr16:82150293-82216622	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv525467	chr16:82154619-82223485	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1061064	chr16:82165314-82213799	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv1056381	chr16:82165314-82215388	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1062687	chr16:82165516-82213799	Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv518129	chr16:82188173-82228076	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv833302	chr16:82188351-82363863	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	esv1844598	chr16:82195234-82429790	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv1847414	chr16:82195234-82429790	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv532600	chr16:82197554-82314289	Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12597171	C1orf64	trans	parietal	SCAN
rs12597171	MPHOSPH6	cis	cerebellum	SCAN
rs12597171	MLYCD	cis	parietal	SCAN
rs12597171	MPHOSPH6	cis	parietal	SCAN
rs12597171	MPHOSPH6	cis	Stomach	GTEx
rs12597171	MPHOSPH6	cis	multi-tissue	Pritchard
rs12597171	MPHOSPH6	cis	Thyroid	GTEx
rs12597171	MPHOSPH6	cis	Artery Tibial	GTEx
rs12597171	VAT1L	cis	cerebellum	SCAN
rs12597171	CLEC3A	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:82173400-82203000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:82186000-82201600	Strong transcription	Primary T cells from cord blood	blood
3	chr16:82186400-82202800	Weak transcription	Psoas Muscle	Psoas
4	chr16:82186600-82202600	Weak transcription	Stomach Mucosa	stomach
5	chr16:82187400-82200600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr16:82188400-82202200	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr16:82191000-82201000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr16:82191200-82200800	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr16:82191200-82201000	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr16:82191400-82201000	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr16:82192000-82200400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr16:82192400-82200800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr16:82192600-82201200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr16:82193000-82200400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr16:82193000-82201600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr16:82193200-82200400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr16:82193200-82200800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr16:82193200-82200800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr16:82193200-82201000	Strong transcription	Fetal Intestine Large	intestine
20	chr16:82193200-82201800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr16:82193400-82200200	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr16:82193400-82200400	Strong transcription	Dnd41	blood
23	chr16:82193400-82200800	Strong transcription	HMEC	breast
24	chr16:82193400-82201200	Strong transcription	Fetal Muscle Leg	muscle
25	chr16:82193400-82201200	Strong transcription	NHLF	lung
26	chr16:82193400-82201400	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr16:82193400-82201600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr16:82193400-82201600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr16:82193400-82201600	Strong transcription	Fetal Stomach	stomach
30	chr16:82193400-82201800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr16:82193400-82201800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr16:82193400-82202000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr16:82193600-82201400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr16:82193800-82200800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr16:82193800-82200800	Strong transcription	Brain Hippocampus Middle	brain
36	chr16:82193800-82202000	Strong transcription	Cortex derived primary cultured neurospheres	brain
37	chr16:82194000-82200400	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr16:82194000-82200800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr16:82194000-82200800	Strong transcription	K562	blood
40	chr16:82194000-82201000	Strong transcription	HSMM	muscle
41	chr16:82194000-82201400	Strong transcription	NHEK	skin
42	chr16:82194000-82201600	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr16:82194400-82200200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr16:82194400-82200400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr16:82194600-82200600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr16:82194600-82201600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr16:82195400-82200200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr16:82195400-82200200	Strong transcription	Colonic Mucosa	Colon
49	chr16:82195800-82202000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr16:82196200-82202200	Weak transcription	Esophagus	oesophagus

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