Variant report

Variant	rs471401
Chromosome Location	chr18:12858321-12858322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:12857931..12860892-chr18:12869007..12871275,2	K562	blood:
2	chr18:12857540..12860632-chr18:12880994..12885408,6	MCF-7	breast:
3	chr18:12857671..12859618-chr18:12882666..12885584,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175354	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs2032174	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2292758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2847288	0.89[JPT][hapmap]
rs3826556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs45579734	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4797707	0.95[ASN][1000 genomes]
rs4797708	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs487273	1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs502763	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs507304	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs513185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs515151	0.96[AFR][1000 genomes]
rs547268	0.93[YRI][hapmap];0.80[AFR][1000 genomes]
rs578377	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58200120	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59471125	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs607906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs612058	0.93[AFR][1000 genomes]
rs622717	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][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]
rs637643	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6505769	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs657555	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs669822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs670671	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs683468	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7238238	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7241650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73950681	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73950683	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73950684	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73950685	0.83[ASN][1000 genomes]
rs8084365	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8091305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8091566	0.81[AFR][1000 genomes]
rs8098730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9954778	0.83[ASN][1000 genomes]
rs9959061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961827	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9961931	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9966378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[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	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv1062014	chr18:12687210-13183383	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv543655	chr18:12687210-13183383	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
4	nsv1064844	chr18:12748045-12953235	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases
5	nsv543656	chr18:12748045-12953235	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12829000-12861200	Weak transcription	Fetal Brain Female	brain
2	chr18:12829000-12862600	Weak transcription	Brain Germinal Matrix	brain
3	chr18:12838600-12861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr18:12838600-12862000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr18:12838600-12862400	Weak transcription	NH-A	brain
6	chr18:12838600-12862600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr18:12838800-12879000	Weak transcription	Psoas Muscle	Psoas
8	chr18:12839400-12861200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr18:12839600-12858800	Weak transcription	Adipose Nuclei	Adipose
10	chr18:12839600-12861200	Weak transcription	Brain Hippocampus Middle	brain
11	chr18:12839600-12862600	Weak transcription	HSMM	muscle
12	chr18:12840000-12863800	Weak transcription	Brain Anterior Caudate	brain
13	chr18:12841000-12859000	Weak transcription	Right Ventricle	heart
14	chr18:12841000-12863200	Weak transcription	Colonic Mucosa	Colon
15	chr18:12841400-12863400	Weak transcription	Esophagus	oesophagus
16	chr18:12843600-12861400	Weak transcription	Fetal Heart	heart
17	chr18:12844200-12879800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr18:12844400-12862600	Weak transcription	K562	blood
19	chr18:12844600-12862400	Weak transcription	Small Intestine	intestine
20	chr18:12847200-12862600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr18:12848800-12858600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr18:12849000-12862600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr18:12849200-12861200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr18:12849200-12861200	Weak transcription	HMEC	breast
25	chr18:12852000-12858600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr18:12852000-12861600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr18:12852000-12863200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr18:12852200-12859000	Weak transcription	Fetal Lung	lung
29	chr18:12852200-12859600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr18:12852400-12861600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr18:12852400-12862600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr18:12852400-12862600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr18:12852400-12863000	Weak transcription	NHLF	lung
34	chr18:12854400-12861800	Weak transcription	Colon Smooth Muscle	Colon
35	chr18:12854400-12862400	Weak transcription	Left Ventricle	heart
36	chr18:12854600-12859600	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr18:12854800-12864000	Weak transcription	Brain Substantia Nigra	brain
38	chr18:12855200-12858400	Strong transcription	Liver	Liver
39	chr18:12855800-12859000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr18:12856000-12858400	Strong transcription	Fetal Kidney	kidney
41	chr18:12856400-12858400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr18:12856400-12861800	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr18:12856400-12862800	Weak transcription	Osteobl	bone
44	chr18:12856600-12859200	Weak transcription	HepG2	liver
45	chr18:12856600-12859400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr18:12856600-12861600	Weak transcription	Pancreas	Pancrea
47	chr18:12856600-12862200	Weak transcription	Placenta	Placenta
48	chr18:12856600-12862400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr18:12856600-12862800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr18:12856600-12863000	Weak transcription	H9 Cell Line	embryonic stem cell

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