Variant report

Variant	rs16957168
Chromosome Location	chr15:43090520-43090521
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43071141..43072690-chr15:43088507..43091296,2	K562	blood:

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10162939	0.90[JPT][hapmap]
rs10518779	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11070378	0.83[YRI][hapmap]
rs1197550	0.90[JPT][hapmap]
rs1197551	0.90[JPT][hapmap]
rs12905385	0.93[ASW][hapmap]
rs12914570	0.90[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap]
rs12917018	0.85[MEX][hapmap]
rs13329197	0.90[ASN][1000 genomes]
rs16957020	0.81[ASW][hapmap];0.85[MEX][hapmap]
rs16957277	0.90[JPT][hapmap]
rs1705356	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs2136899	0.86[ASW][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2136900	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2139655	0.83[YRI][hapmap]
rs2175370	0.90[JPT][hapmap]
rs2305084	1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[ASN][1000 genomes]
rs2305085	0.85[YRI][hapmap]
rs2412748	0.81[EUR][1000 genomes]
rs28498538	0.85[ASN][1000 genomes]
rs28562951	0.85[ASN][1000 genomes]
rs28609797	0.86[EUR][1000 genomes]
rs28613047	0.86[EUR][1000 genomes]
rs28620320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28744617	0.83[ASN][1000 genomes]
rs28796057	0.86[EUR][1000 genomes]
rs28810091	0.86[EUR][1000 genomes]
rs28871732	0.86[EUR][1000 genomes]
rs3099758	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs3742993	0.80[ASW][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4924694	0.83[MEX][hapmap]
rs4924699	0.80[CEU][hapmap]
rs623271	0.90[JPT][hapmap]
rs6493059	0.81[ASW][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[ASN][1000 genomes]
rs6493063	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6493066	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs66947001	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs672054	0.90[JPT][hapmap]
rs7166775	0.81[CEU][hapmap]
rs7167392	0.81[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs7169009	0.85[MEX][hapmap]
rs7175582	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs7176860	0.85[ASN][1000 genomes]
rs7178248	0.84[EUR][1000 genomes]
rs7181859	0.86[EUR][1000 genomes]
rs7182141	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7182515	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8024266	0.83[YRI][hapmap]
rs8024902	0.90[JPT][hapmap]
rs8028785	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs8031218	0.84[MEX][hapmap]
rs8037613	0.80[CEU][hapmap]
rs8039711	0.90[JPT][hapmap]
rs8039765	0.90[JPT][hapmap];0.84[MEX][hapmap]
rs9269	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs938047	0.90[JPT][hapmap]
rs9783713	1.00[ASN][1000 genomes]
rs9919994	1.00[JPT][hapmap];1.00[MEX][hapmap]
rs9920163	0.90[JPT][hapmap];0.85[MEX][hapmap]
rs9920182	0.94[ASW][hapmap];0.95[CEU][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs9920202	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]

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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers 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	10 gene(s)	inside rSNPs	diseases
3	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16957168	CDAN1	cis	parietal	SCAN
rs16957168	MAP1A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43030000-43093600	Weak transcription	Colonic Mucosa	Colon
2	chr15:43053600-43112200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:43056800-43116800	Weak transcription	HepG2	liver
5	chr15:43057600-43107000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:43060800-43122200	Weak transcription	GM12878-XiMat	blood
7	chr15:43063000-43093000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:43063400-43093600	Weak transcription	Esophagus	oesophagus
9	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
10	chr15:43064000-43114200	Weak transcription	Fetal Kidney	kidney
11	chr15:43064800-43150800	Weak transcription	HSMM	muscle
12	chr15:43066400-43095600	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr15:43066600-43097600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:43067400-43147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:43067600-43092800	Weak transcription	Brain Germinal Matrix	brain
16	chr15:43067800-43093000	Weak transcription	Fetal Brain Female	brain
17	chr15:43067800-43095200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr15:43068000-43093000	Weak transcription	Spleen	Spleen
19	chr15:43068400-43093000	Weak transcription	Aorta	Aorta
20	chr15:43068400-43093600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr15:43068800-43092600	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:43069000-43092800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:43069000-43093400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:43075200-43092600	Weak transcription	Fetal Heart	heart
25	chr15:43075200-43093600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:43075200-43143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:43075400-43135800	Weak transcription	HSMMtube	muscle
28	chr15:43075600-43093000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:43075600-43093400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:43075600-43093600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:43075600-43093600	Weak transcription	Fetal Lung	lung
32	chr15:43075600-43093600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:43075600-43150800	Weak transcription	Colon Smooth Muscle	Colon
34	chr15:43075800-43092600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:43075800-43093000	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:43075800-43093000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr15:43075800-43093000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr15:43075800-43093000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:43075800-43093000	Weak transcription	Left Ventricle	heart
40	chr15:43075800-43093000	Weak transcription	Lung	lung
41	chr15:43075800-43093000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr15:43075800-43093200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:43075800-43093200	Weak transcription	Primary B cells from peripheral blood	blood
44	chr15:43075800-43093200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr15:43075800-43093200	Weak transcription	Right Ventricle	heart
46	chr15:43075800-43093200	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:43075800-43093400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:43075800-43093400	Weak transcription	Ovary	ovary
49	chr15:43075800-43093600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:43075800-43093600	Weak transcription	Brain Substantia Nigra	brain

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