Variant report

Variant	rs4662703
Chromosome Location	chr2:127800981-127800982
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:127781170..127783496-chr2:127799627..127801145,2	K562	blood:
2	chr2:127800876..127803938-chr2:127806149..127808710,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260634	Chromatin interaction
ENSG00000260163	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11888878	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11893989	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11902275	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12465042	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12474412	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12476339	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12477924	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17014784	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17014818	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17014851	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17040070	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2071268	0.96[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2071270	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3768859	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3768860	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3820757	0.87[MEX][hapmap]
rs4663089	0.96[CEU][hapmap]
rs4663090	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55819047	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55999604	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56408880	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60022219	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66507470	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6745677	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs67920725	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72481904	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs727095	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72846676	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7570116	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7573824	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs880436	0.96[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv459230	chr2:127771006-127844735	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv583032	chr2:127771006-127844735	Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1003730	chr2:127794288-127860830	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1003461	chr2:127794288-127862257	Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv516759	chr2:127796666-127859441	Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
8	nsv1000994	chr2:127797089-127860830	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	esv1825024	chr2:127798138-127864285	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv3407788	chr2:127799382-127804180	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3434419	chr2:127800182-127803480	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3369639	chr2:127800182-127803580	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	esv3413457	chr2:127800282-127803480	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv459241	chr2:127800981-127868435	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv583033	chr2:127800981-127868435	Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv875011	chr2:127800981-127868435	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv875012	chr2:127800981-127895573	Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4662703	AMMECR1L	cis	parietal	SCAN
rs4662703	MYO7B	cis	parietal	SCAN
rs4662703	POLR2D	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127783800-127815600	Weak transcription	Aorta	Aorta
2	chr2:127793200-127801200	Weak transcription	Fetal Lung	lung
3	chr2:127793200-127805400	Weak transcription	Liver	Liver
4	chr2:127795600-127801400	Weak transcription	Fetal Heart	heart
5	chr2:127795800-127807600	Weak transcription	Brain Germinal Matrix	brain
6	chr2:127797600-127805200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:127797800-127803600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:127797800-127805600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:127798200-127811400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr2:127799400-127801400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:127799400-127804800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr2:127799600-127801800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:127799600-127803800	Weak transcription	Right Ventricle	heart
14	chr2:127799600-127805800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:127799600-127805800	Weak transcription	Gastric	stomach
16	chr2:127799600-127806200	Weak transcription	Brain Angular Gyrus	brain
17	chr2:127799800-127801200	Weak transcription	Fetal Kidney	kidney
18	chr2:127800000-127807600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:127800200-127807400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr2:127800400-127802000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:127800600-127801400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:127800600-127801400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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