Variant report

Variant	rs17400980
Chromosome Location	chr2:153597798-153597799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:153597440..153598293-chr2:154375099..154375934,2	K562	blood:
2	chr2:153575200..153576038-chr2:153597312..153597856,2	MCF-7	breast:
3	chr2:153576417..153577088-chr2:153597271..153597951,2	MCF-7	breast:
4	chr2:153589125..153592910-chr2:153595125..153598674,4	K562	blood:
5	chr2:153597391..153597936-chr2:154334957..154335467,2	K562	blood:
6	chr2:153572156..153572973-chr2:153596946..153597899,5	MCF-7	breast:
7	chr2:153572370..153575130-chr2:153597326..153599470,2	MCF-7	breast:
8	chr2:153548570..153551417-chr2:153597011..153599645,2	MCF-7	breast:
9	chr2:153597123..153597921-chr2:154334933..154335784,3	MCF-7	breast:
10	chr2:153573681..153576550-chr2:153596257..153599415,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000177519	Chromatin interaction
ENSG00000196504	Chromatin interaction
ENSG00000177917	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10497113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931263	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931279	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1135617	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676069	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694512	0.84[ASN][1000 genomes]
rs11901227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478681	0.84[ASN][1000 genomes]
rs12693429	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs12989903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990935	1.00[CHB][hapmap]
rs12995388	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13003670	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13006652	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022436	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023779	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1370499	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831456	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17328776	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400456	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400952	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083097	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34199006	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34454505	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34619076	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775858	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002744	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35421285	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754252	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894330	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35937874	0.86[EUR][1000 genomes]
rs36107565	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36122595	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811568	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811569	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4575677	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434172	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492085	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66849546	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728189	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736003	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417232	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417235	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72871148	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591590	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1798142	chr2:153578113-153600123	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv875293	chr2:153578900-153617420	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv834422	chr2:153589448-153743069	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153575800-153611600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:153575800-153611600	Weak transcription	Esophagus	oesophagus
3	chr2:153575800-153621400	Weak transcription	Pancreas	Pancrea
4	chr2:153576000-153615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:153577200-153617600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:153577600-153617800	Weak transcription	NHLF	lung
7	chr2:153578600-153605800	Weak transcription	Fetal Heart	heart
8	chr2:153579600-153602000	Weak transcription	Fetal Brain Male	brain
9	chr2:153579800-153599800	Weak transcription	A549	lung
10	chr2:153582000-153610600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr2:153583000-153611600	Weak transcription	Lung	lung
12	chr2:153587400-153603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr2:153587400-153608800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:153587400-153610600	Weak transcription	Small Intestine	intestine
15	chr2:153587600-153599800	Weak transcription	Stomach Mucosa	stomach
16	chr2:153587600-153602000	Weak transcription	Hela-S3	cervix
17	chr2:153587600-153618000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:153587600-153621600	Weak transcription	NHEK	skin
19	chr2:153588000-153617800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:153588200-153618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:153588600-153619400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:153589400-153613600	Weak transcription	Brain Angular Gyrus	brain
23	chr2:153589600-153601600	Weak transcription	Brain Substantia Nigra	brain
24	chr2:153590200-153616800	Weak transcription	Right Ventricle	heart
25	chr2:153590400-153620400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:153591000-153611800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:153592200-153618800	Weak transcription	HSMMtube	muscle
28	chr2:153593200-153618800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:153593200-153628400	Weak transcription	Fetal Kidney	kidney
30	chr2:153593600-153598400	Weak transcription	NHDF-Ad	bronchial
31	chr2:153593600-153617000	Weak transcription	Brain Anterior Caudate	brain
32	chr2:153593600-153618600	Weak transcription	Osteobl	bone
33	chr2:153593600-153621800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr2:153593800-153602000	Weak transcription	GM12878-XiMat	blood
35	chr2:153593800-153606600	Weak transcription	Liver	Liver
36	chr2:153593800-153608000	Weak transcription	HSMM	muscle
37	chr2:153593800-153613400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:153593800-153617600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:153593800-153617600	Weak transcription	NH-A	brain
40	chr2:153593800-153620000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr2:153593800-153621400	Weak transcription	HMEC	breast
42	chr2:153593800-153621600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:153594000-153603400	Weak transcription	Primary B cells from cord blood	blood
44	chr2:153594200-153613400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:153594400-153598600	Weak transcription	HUVEC	blood vessel
46	chr2:153594400-153615000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:153594800-153606200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:153595200-153598200	Weak transcription	K562	blood
49	chr2:153595200-153599200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr2:153595200-153599800	Weak transcription	Colon Smooth Muscle	Colon

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