Variant report

Variant	rs452138
Chromosome Location	chr2:40435566-40435567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr2:40435526-40435940	MCF-7	breast:	n/a	chr2:40435812-40435829 chr2:40435809-40435826 chr2:40435816-40435825 chr2:40435814-40435827 chr2:40435813-40435828 chr2:40435811-40435825 chr2:40435816-40435827 chr2:40435815-40435829
2	SRF	chr2:40435509-40436052	MCF-7	breast:	n/a	chr2:40435812-40435829 chr2:40435809-40435826 chr2:40435816-40435825 chr2:40435814-40435827 chr2:40435813-40435828 chr2:40435811-40435825 chr2:40435816-40435827 chr2:40435815-40435829

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40430449..40432032-chr2:40434397..40435947,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM178-2	chr2:40435515-40435591	ENSG00000227028.2

Variant related genes	Relation type
SLC8A1-AS1	TF binding region

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

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs105288	0.88[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1641452	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1641456	0.83[ASN][1000 genomes]
rs1641457	0.83[ASN][1000 genomes]
rs1641458	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1651355	0.83[ASN][1000 genomes]
rs1651356	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34971853	0.83[ASN][1000 genomes]
rs36162999	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36184451	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs366578	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs368642	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs369140	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs371909	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs372052	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs373606	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs374159	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs374711	0.84[ASN][1000 genomes]
rs3749056	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs375180	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs376170	0.83[ASN][1000 genomes]
rs376491	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs379410	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs379859	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs380082	0.85[ASW][hapmap];0.82[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap]
rs380975	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs383073	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs384511	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs384791	0.83[ASN][1000 genomes]
rs384994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs385561	0.84[ASW][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389109	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs391631	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs391984	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs393711	0.86[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs394112	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[YRI][hapmap]
rs394540	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs399061	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs402307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs405884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs406222	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[YRI][hapmap]
rs406736	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406880	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs407267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407388	0.85[ASW][hapmap];1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[YRI][hapmap]
rs407889	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs408009	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs408662	0.84[ASN][1000 genomes]
rs410480	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs413711	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs415695	0.82[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs417464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs417591	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs417873	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs418380	0.83[ASN][1000 genomes]
rs418780	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs421870	1.00[JPT][hapmap]
rs422411	0.81[ASN][1000 genomes]
rs423075	0.84[ASN][1000 genomes]
rs426295	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs427632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs428738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs429227	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430314	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs430394	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs430473	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs432142	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs432769	1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs432981	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434082	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs434326	0.83[ASN][1000 genomes]
rs436010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[ASN][1000 genomes]
rs439960	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs440155	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs441196	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs441413	0.88[CHB][hapmap];0.90[JPT][hapmap]
rs441593	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs441802	0.85[ASN][1000 genomes]
rs442476	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs442586	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs443236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs444504	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs450116	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs450823	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs451074	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs451158	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs451811	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs479909	0.97[ASN][1000 genomes]
rs4952596	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs505473	0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap]
rs581477	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs581568	1.00[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.81[ASN][1000 genomes]
rs588179	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs615449	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[ASN][1000 genomes]
rs666362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs678107	1.00[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs679339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs688673	0.88[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs72794789	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873910	chr2:40391907-40466268	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv1851152	chr2:40393223-40512023	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv526425	chr2:40418386-40447587	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv526074	chr2:40423454-40451724	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1008190	chr2:40429442-40506772	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40418200-40447200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr2:40418600-40445800	Weak transcription	Dnd41	blood
3	chr2:40419200-40436600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:40422600-40436400	Weak transcription	Right Ventricle	heart
5	chr2:40430600-40439600	Weak transcription	HSMM	muscle
6	chr2:40430800-40439800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:40431200-40436400	Weak transcription	Left Ventricle	heart
8	chr2:40431200-40440600	Weak transcription	Fetal Stomach	stomach
9	chr2:40431400-40439800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:40431400-40440200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:40431600-40436400	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:40431800-40440000	Weak transcription	NHDF-Ad	bronchial
13	chr2:40432200-40440200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:40434200-40437200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:40434600-40437200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:40434800-40435800	Enhancers	Fetal Heart	heart
17	chr2:40435000-40435600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:40435000-40435800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:40435000-40436000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:40435000-40436000	Enhancers	Osteobl	bone
21	chr2:40435200-40435800	Enhancers	Fetal Kidney	kidney

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