Variant report

Variant	rs17400952
Chromosome Location	chr2:153592116-153592117
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:153589125..153592910-chr2:153595125..153598674,4	K562	blood:
2	chr2:153574438..153578622-chr2:153591966..153593702,3	MCF-7	breast:
3	chr2:153586570..153588683-chr2:153591987..153594284,2	K562	blood:
4	chr2:153564281..153565931-chr2:153590243..153592879,2	K562	blood:
5	chr2:153586570..153590244-chr2:153591185..153594577,6	K562	blood:
6	chr2:153572903..153577079-chr2:153590575..153593483,4	K562	blood:

Variant related genes	Relation type
ENSG00000177917	Chromatin interaction
ENSG00000196504	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10497113	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931263	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931271	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931279	0.88[AMR][1000 genomes]
rs1135617	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674911	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676069	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11694512	0.84[ASN][1000 genomes]
rs11901227	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475871	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12478681	0.84[ASN][1000 genomes]
rs12693429	0.84[ASN][1000 genomes]
rs12989903	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12995388	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12999331	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13003670	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13006652	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13014141	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017131	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13022436	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13023779	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1370499	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831456	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17328776	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400456	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17400938	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17400980	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	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34199006	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34454505	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34619076	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34775858	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35002744	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35421285	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35754252	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35894330	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35937874	0.82[EUR][1000 genomes]
rs36107565	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36122595	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811568	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3811569	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4575677	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434172	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66492085	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66849546	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6728189	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6736003	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417232	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71417235	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72871148	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591590	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598878	0.97[AMR][1000 genomes];0.90[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:121 , 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	chr2:153576000-153594400	Weak transcription	Left Ventricle	heart
5	chr2:153576000-153615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:153576200-153594800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:153576800-153592600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:153576800-153592800	Weak transcription	NH-A	brain
9	chr2:153577000-153592600	Weak transcription	Fetal Intestine Large	intestine
10	chr2:153577000-153592800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:153577000-153593000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:153577000-153593000	Weak transcription	Osteobl	bone
13	chr2:153577000-153594400	Weak transcription	Aorta	Aorta
14	chr2:153577000-153594600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:153577000-153595000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:153577200-153592800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:153577200-153593000	Weak transcription	Fetal Kidney	kidney
18	chr2:153577200-153593000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:153577200-153593400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:153577200-153594200	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:153577200-153594600	Weak transcription	Spleen	Spleen
22	chr2:153577200-153617600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:153577400-153593000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:153577400-153593400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:153577600-153594200	Weak transcription	Fetal Intestine Small	intestine
26	chr2:153577600-153617800	Weak transcription	NHLF	lung
27	chr2:153577800-153592800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:153577800-153593000	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:153577800-153593000	Weak transcription	Ovary	ovary
30	chr2:153577800-153594800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr2:153578200-153593400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr2:153578600-153605800	Weak transcription	Fetal Heart	heart
33	chr2:153578800-153592800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr2:153578800-153592800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:153579000-153592600	Weak transcription	HUVEC	blood vessel
36	chr2:153579200-153593400	Weak transcription	Fetal Brain Female	brain
37	chr2:153579600-153602000	Weak transcription	Fetal Brain Male	brain
38	chr2:153579800-153599800	Weak transcription	A549	lung
39	chr2:153581400-153593000	Weak transcription	K562	blood
40	chr2:153581600-153593400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:153582000-153610600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr2:153583000-153593000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:153583000-153611600	Weak transcription	Lung	lung
44	chr2:153584400-153592800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:153584400-153592800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:153585800-153594200	Weak transcription	Fetal Stomach	stomach
47	chr2:153587400-153594000	Weak transcription	Gastric	stomach
48	chr2:153587400-153594200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:153587400-153595600	Weak transcription	Psoas Muscle	Psoas
50	chr2:153587400-153603800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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