Variant report

Variant	rs12740860
Chromosome Location	chr1:10896954-10896955
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:10895780..10898598-chr1:10906718..10908430,2	K562	blood:
2	chr1:10882954..10889403-chr1:10891369..10897064,9	MCF-7	breast:
3	chr1:10892493..10894572-chr1:10896647..10899321,2	MCF-7	breast:
4	chr1:10895281..10897495-chr1:11000321..11002015,2	MCF-7	breast:
5	chr1:10674874..10677843-chr1:10895529..10897337,2	K562	blood:
6	chr1:10837835..10840476-chr1:10895758..10897278,2	MCF-7	breast:
7	chr1:10895780..10898681-chr1:10906620..10908430,2	K562	blood:
8	chr1:10895615..10898736-chr1:10923813..10928307,5	K562	blood:
9	chr1:10880964..10882557-chr1:10895736..10897488,2	MCF-7	breast:
10	chr1:10874336..10876835-chr1:10896377..10898492,2	MCF-7	breast:
11	chr1:10890948..10893091-chr1:10894513..10897214,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000243267	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11578562	1.00[AFR][1000 genomes]
rs12028719	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12030479	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12048262	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12048967	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12142503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12143767	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724489	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12724989	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12731652	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617195	1.00[ASN][1000 genomes]
rs1776218	1.00[ASN][1000 genomes]
rs1776219	1.00[ASN][1000 genomes]
rs34217099	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34542452	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34593019	1.00[AFR][1000 genomes]
rs34896200	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35126763	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35261279	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35414554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35677622	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35858703	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36047809	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71509068	1.00[AFR][1000 genomes]
rs71509069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72864610	1.00[ASN][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	nsv529981	chr1:10697093-11353487	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	esv2757723	chr1:10742502-11055147	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2758921	chr1:10742502-11055147	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv870589	chr1:10840905-10901994	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv871617	chr1:10858746-10935232	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv871155	chr1:10858746-10998509	Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	esv1825837	chr1:10887923-11093741	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10883600-10902800	Weak transcription	Right Atrium	heart
2	chr1:10895000-10900200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:10895200-10900200	Enhancers	Brain Germinal Matrix	brain
4	chr1:10895600-10897800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:10895600-10897800	Bivalent Enhancer	Placenta	Placenta
6	chr1:10895800-10897600	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr1:10895800-10897800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
8	chr1:10896000-10897400	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:10896000-10897600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:10896000-10897600	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:10896000-10899000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:10896000-10899400	Bivalent Enhancer	Fetal Muscle Leg	muscle
13	chr1:10896000-10900200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr1:10896000-10900200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr1:10896200-10897600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:10896200-10897800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:10896400-10897000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr1:10896400-10897200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:10896400-10897600	Weak transcription	Fetal Heart	heart
20	chr1:10896400-10899000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:10896400-10899400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr1:10896400-10900200	Weak transcription	Pancreas	Pancrea
23	chr1:10896400-10901200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr1:10896600-10897400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr1:10896600-10897800	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr1:10896800-10897600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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