Variant report

Variant	rs1515873
Chromosome Location	chr2:190030345-190030346
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190016341..190018052-chr2:190028651..190030939,2	MCF-7	breast:
2	chr2:190029422..190031666-chr2:190149954..190151681,2	MCF-7	breast:
3	chr2:190030141..190032156-chr2:190304777..190307765,2	MCF-7	breast:
4	chr2:190027832..190030639-chr2:190032693..190035632,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115368	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10174225	0.83[ASN][1000 genomes]
rs10177513	0.83[ASN][1000 genomes]
rs10497699	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10931402	0.82[ASN][1000 genomes]
rs10931406	0.82[ASN][1000 genomes]
rs10931410	0.82[ASN][1000 genomes]
rs11675295	0.82[ASN][1000 genomes]
rs11676812	0.83[ASN][1000 genomes]
rs11677073	0.82[ASN][1000 genomes]
rs11678388	0.85[ASN][1000 genomes]
rs11681937	0.82[ASN][1000 genomes]
rs11684417	0.82[ASN][1000 genomes]
rs11684869	0.82[ASN][1000 genomes]
rs11687908	0.82[ASN][1000 genomes]
rs11693810	0.82[ASN][1000 genomes]
rs12472232	0.88[ASN][1000 genomes]
rs1515875	0.85[ASN][1000 genomes]
rs1519185	0.82[ASN][1000 genomes]
rs1520862	0.82[ASN][1000 genomes]
rs17198773	0.82[ASN][1000 genomes]
rs17198780	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17198787	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17198815	0.82[ASN][1000 genomes]
rs17198829	0.82[ASN][1000 genomes]
rs17270952	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17270966	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17270973	0.85[ASN][1000 genomes]
rs17271015	0.82[ASN][1000 genomes]
rs1996576	0.82[ASN][1000 genomes]
rs2680629	0.83[ASN][1000 genomes]
rs2683013	0.82[ASN][1000 genomes]
rs2683014	0.82[ASN][1000 genomes]
rs2683015	0.83[ASN][1000 genomes]
rs2683016	0.83[ASN][1000 genomes]
rs35598715	0.82[ASN][1000 genomes]
rs55726777	0.84[ASN][1000 genomes]
rs55851872	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59031473	0.82[ASN][1000 genomes]
rs61130121	0.88[ASN][1000 genomes]
rs61528955	0.82[ASN][1000 genomes]
rs62182060	0.82[ASN][1000 genomes]
rs62182061	0.82[ASN][1000 genomes]
rs62182066	0.82[ASN][1000 genomes]
rs62182067	0.83[ASN][1000 genomes]
rs62182068	0.82[ASN][1000 genomes]
rs62182069	0.82[ASN][1000 genomes]
rs62182415	0.82[ASN][1000 genomes]
rs62182420	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62182421	0.82[ASN][1000 genomes]
rs62182454	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62182457	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62182458	0.83[ASN][1000 genomes]
rs62183794	0.82[ASN][1000 genomes]
rs62183841	0.82[ASN][1000 genomes]
rs62183844	0.82[ASN][1000 genomes]
rs62183845	0.82[ASN][1000 genomes]
rs62183846	0.82[ASN][1000 genomes]
rs62183848	0.82[ASN][1000 genomes]
rs72908368	0.88[ASN][1000 genomes]
rs72908382	0.88[ASN][1000 genomes]
rs72910347	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72910360	0.81[EUR][1000 genomes]
rs72912280	0.82[ASN][1000 genomes]
rs72912286	0.82[ASN][1000 genomes]
rs72914141	0.82[ASN][1000 genomes]
rs7564429	0.82[ASN][1000 genomes]
rs7577872	0.84[ASN][1000 genomes]
rs7586853	0.88[ASN][1000 genomes]
rs9808245	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv875613	chr2:189999011-190324685	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190019600-190040000	Weak transcription	Fetal Intestine Small	intestine
2	chr2:190021000-190031400	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:190026600-190032000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:190026800-190030800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:190027200-190030800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:190027600-190032000	Enhancers	Fetal Lung	lung
7	chr2:190027800-190031400	Enhancers	NH-A	brain
8	chr2:190028000-190030800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:190028000-190032800	Enhancers	NHLF	lung
10	chr2:190028200-190030400	Enhancers	Hela-S3	cervix
11	chr2:190028200-190030600	Enhancers	Adipose Nuclei	Adipose
12	chr2:190028400-190030600	Enhancers	Fetal Stomach	stomach
13	chr2:190028400-190033800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:190028600-190030800	Enhancers	NHDF-Ad	bronchial
15	chr2:190028800-190034200	Enhancers	Liver	Liver
16	chr2:190029000-190030600	Weak transcription	Colon Smooth Muscle	Colon
17	chr2:190029000-190030800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr2:190029000-190030800	Weak transcription	Aorta	Aorta
19	chr2:190029000-190031200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr2:190029000-190031400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:190029000-190033600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:190029000-190037200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr2:190029200-190031200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:190029200-190033600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:190029400-190040800	Weak transcription	Fetal Kidney	kidney
26	chr2:190029400-190042200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:190029600-190030400	Enhancers	Ovary	ovary
28	chr2:190029600-190030400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr2:190029600-190030600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr2:190029600-190031000	Weak transcription	HSMMtube	muscle
31	chr2:190029600-190032600	Enhancers	Fetal Muscle Leg	muscle
32	chr2:190029600-190043400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:190029800-190030800	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:190029800-190030800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:190029800-190031400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:190029800-190031400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:190029800-190031400	Weak transcription	HMEC	breast
38	chr2:190029800-190033600	Enhancers	A549	lung
39	chr2:190029800-190036800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr2:190029800-190043200	Weak transcription	Psoas Muscle	Psoas
41	chr2:190030000-190032000	Genic enhancers	HSMM	muscle
42	chr2:190030000-190036600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:190030000-190041200	Weak transcription	HUVEC	blood vessel
44	chr2:190030200-190030400	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr2:190030200-190030400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr2:190030200-190030600	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:190030200-190030600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr2:190030200-190031000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:190030200-190031000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr2:190030200-190031400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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