Variant report

Variant	rs13406929
Chromosome Location	chr2:55521312-55521313
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55494684..55499569-chr2:55516943..55523168,5	K562	blood:
2	chr2:55513717..55517670-chr2:55518024..55521740,6	K562	blood:
3	chr2:55520326..55522931-chr2:55543015..55545040,2	K562	blood:
4	chr2:55510957..55512657-chr2:55520415..55521941,2	MCF-7	breast:
5	chr2:55516323..55518543-chr2:55519705..55522425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115355	Chromatin interaction
ENSG00000085760	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10153861	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10181997	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10184362	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10186158	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10191785	0.94[YRI][hapmap];0.91[AFR][1000 genomes]
rs10194658	0.90[AFR][1000 genomes]
rs10196295	0.90[AFR][1000 genomes]
rs10199332	1.00[EUR][1000 genomes]
rs10201075	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10202943	0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10209908	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10518764	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes]
rs13383527	1.00[EUR][1000 genomes]
rs13384739	0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13389151	1.00[EUR][1000 genomes]
rs13389799	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13390100	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs13398447	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13402277	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs13404740	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13405460	1.00[EUR][1000 genomes]
rs13408706	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13411077	1.00[EUR][1000 genomes]
rs13411257	1.00[EUR][1000 genomes]
rs13412682	0.90[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13416519	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13417988	1.00[EUR][1000 genomes]
rs13419337	1.00[EUR][1000 genomes]
rs13424499	1.00[EUR][1000 genomes]
rs13426160	0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13426766	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs13429863	1.00[EUR][1000 genomes]
rs1545554	0.82[LWK][hapmap]
rs17046801	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17046820	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17046828	0.93[ASW][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046829	1.00[EUR][1000 genomes]
rs17046835	1.00[EUR][1000 genomes]
rs17046837	0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17046881	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046896	0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17046898	1.00[EUR][1000 genomes]
rs17046954	1.00[EUR][1000 genomes]
rs17046959	1.00[EUR][1000 genomes]
rs17046963	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17046964	1.00[EUR][1000 genomes]
rs17264948	0.92[YRI][hapmap];0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1902057	0.82[LWK][hapmap]
rs2043716	1.00[EUR][1000 genomes]
rs2123983	0.82[LWK][hapmap]
rs28434193	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28498550	1.00[EUR][1000 genomes]
rs3099080	0.83[LWK][hapmap]
rs3861571	0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs3975804	0.84[YRI][hapmap];1.00[EUR][1000 genomes]
rs56201519	1.00[EUR][1000 genomes]
rs57623398	1.00[EUR][1000 genomes]
rs59695161	1.00[EUR][1000 genomes]
rs60920006	1.00[EUR][1000 genomes]
rs6545485	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6545486	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6704701	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6707774	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710128	1.00[EUR][1000 genomes]
rs6714932	1.00[EUR][1000 genomes]
rs6715991	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6719677	1.00[EUR][1000 genomes]
rs6726757	1.00[EUR][1000 genomes]
rs6729144	0.92[ASW][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6734415	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6735009	1.00[EUR][1000 genomes]
rs6738517	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs6741630	1.00[EUR][1000 genomes]
rs6746757	0.93[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs6746983	0.93[ASW][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs6747974	0.92[YRI][hapmap];0.91[AFR][1000 genomes]
rs6748541	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6754036	1.00[EUR][1000 genomes]
rs6758229	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759625	0.93[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759763	0.92[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6759957	0.92[AFR][1000 genomes]
rs6761771	0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918961	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918964	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918965	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72918972	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72918975	1.00[EUR][1000 genomes]
rs72923130	1.00[EUR][1000 genomes]
rs72923156	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923157	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72923183	1.00[EUR][1000 genomes]
rs72923187	1.00[EUR][1000 genomes]
rs72923194	1.00[EUR][1000 genomes]
rs72923197	1.00[EUR][1000 genomes]
rs72924917	1.00[EUR][1000 genomes]
rs72924922	1.00[EUR][1000 genomes]
rs72927340	1.00[EUR][1000 genomes]
rs72927384	1.00[EUR][1000 genomes]
rs72927388	1.00[EUR][1000 genomes]
rs72929306	1.00[EUR][1000 genomes]
rs7561604	1.00[EUR][1000 genomes]
rs7562535	1.00[EUR][1000 genomes]
rs7577510	0.92[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7589558	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7594907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7606361	0.82[LWK][hapmap]
rs9309264	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv874156	chr2:55474026-55636351	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv874157	chr2:55483020-55571085	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874158	chr2:55513738-55619923	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv874159	chr2:55513738-55636351	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv457941	chr2:55517491-55585915	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv582030	chr2:55517491-55585915	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55509000-55541200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55509400-55545200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:55509600-55522600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:55509800-55521800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:55510000-55521600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:55510000-55521600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:55510000-55521800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:55510000-55521800	Weak transcription	Fetal Brain Male	brain
9	chr2:55510000-55521800	Weak transcription	NHEK	skin
10	chr2:55510000-55522000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:55510000-55522200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:55510000-55522200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:55510000-55522400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:55510000-55522400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:55510000-55522600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr2:55510000-55541600	Weak transcription	Esophagus	oesophagus
17	chr2:55510000-55553600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:55510000-55578800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:55510200-55521800	Weak transcription	Fetal Kidney	kidney
20	chr2:55510200-55522200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:55510200-55522400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:55510200-55522400	Weak transcription	NHLF	lung
23	chr2:55510200-55522600	Weak transcription	Aorta	Aorta
24	chr2:55510200-55542200	Weak transcription	Fetal Intestine Large	intestine
25	chr2:55510200-55559000	Weak transcription	Psoas Muscle	Psoas
26	chr2:55510200-55616800	Weak transcription	Fetal Intestine Small	intestine
27	chr2:55510400-55522400	Weak transcription	Left Ventricle	heart
28	chr2:55510400-55529000	Weak transcription	Placenta	Placenta
29	chr2:55510600-55521800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:55510600-55522400	Weak transcription	A549	lung
31	chr2:55510600-55533800	Weak transcription	Pancreas	Pancrea
32	chr2:55510600-55536600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr2:55510600-55537400	Weak transcription	Lung	lung
34	chr2:55510800-55521800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:55510800-55542200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr2:55511000-55521600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:55511000-55521800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr2:55511000-55521800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:55511000-55540600	Weak transcription	Spleen	Spleen
40	chr2:55511200-55521800	Weak transcription	Liver	Liver
41	chr2:55511200-55521800	Weak transcription	Brain Hippocampus Middle	brain
42	chr2:55511200-55521800	Weak transcription	Thymus	Thymus
43	chr2:55511200-55522200	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:55511200-55542200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:55511200-55547000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:55511400-55521800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:55511400-55522200	Weak transcription	Primary T cells from cord blood	blood
48	chr2:55511600-55521800	Weak transcription	K562	blood
49	chr2:55512000-55549800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:55512400-55577400	Weak transcription	Right Ventricle	heart

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