Variant report

Variant	rs12754677
Chromosome Location	chr1:227421980-227421981
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227421745..227423708-chr1:227616261..227618228,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADCK3-6	chr1:227421970-227422486	NONHSAT009917

Variant related genes	Relation type
ENSG00000242757	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10916112	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10916113	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10916116	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10916125	0.96[AMR][1000 genomes]
rs11576239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11584325	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11585910	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12119153	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12123597	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12128174	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131061	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12131459	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131933	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12133230	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12133633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138092	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12138364	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138383	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138664	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12144205	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12746316	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12755770	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513607	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1513613	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17613235	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2063661	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28648445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34113967	1.00[AMR][1000 genomes]
rs34702208	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34897490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35160496	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35952573	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308948	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61834323	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61834324	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61834326	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61834590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834625	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61834626	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6660168	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675572	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6678714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6697583	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7512871	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7518813	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7523759	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7539662	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7543419	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7548118	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	esv2830098	chr1:227295716-227422234	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227386200-227433400	Weak transcription	Fetal Stomach	stomach
2	chr1:227400400-227426800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:227402400-227430600	Weak transcription	Pancreas	Pancrea
4	chr1:227407200-227432400	Weak transcription	Right Ventricle	heart
5	chr1:227411800-227430600	Weak transcription	Right Atrium	heart
6	chr1:227411800-227431400	Weak transcription	Fetal Intestine Small	intestine
7	chr1:227414000-227424400	Weak transcription	Psoas Muscle	Psoas
8	chr1:227414000-227433200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:227414200-227423400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:227414200-227424200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:227414200-227424400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:227414200-227426800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:227414200-227433400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:227414200-227453800	Weak transcription	HSMM	muscle
16	chr1:227414400-227422200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:227414400-227422400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:227414400-227422400	Weak transcription	K562	blood
19	chr1:227414400-227423000	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr1:227414400-227423000	Weak transcription	Brain Substantia Nigra	brain
21	chr1:227414400-227423600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:227414400-227432400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:227414400-227432600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:227415400-227422200	Weak transcription	Brain Anterior Caudate	brain
25	chr1:227415400-227424400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:227415600-227422800	Weak transcription	HUVEC	blood vessel
27	chr1:227415800-227456800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:227416200-227431800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:227420800-227434600	Weak transcription	Spleen	Spleen
30	chr1:227421800-227422000	Enhancers	Gastric	stomach
31	chr1:227421800-227422000	Enhancers	Ovary	ovary
32	chr1:227421800-227422000	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:227421800-227423000	Enhancers	Left Ventricle	heart

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