Variant report

Variant	rs1054626
Chromosome Location	chr1:94800194-94800195
allele	C/T
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:1)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94524835..94527724-chr1:94798552..94800345,2	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABCD3-2	chr1:94800068-94800425	XLOC_000301
2	lnc-ABCD3-2	chr1:94800068-94800251	XLOC_000301
3	lnc-ABCD3-2	chr1:94800068-94800354	XLOC_000301
4	lnc-ABCD3-2	chr1:94800068-94800404	XLOC_000301
5	lnc-ABCD3-2	chr1:94800068-94800394	NONHSAT004580
6	lnc-ABCD3-2	chr1:94800068-94800394	NONHSAT004579

No data

Variant related genes	Relation type
ENSG00000198691	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11165103	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11165114	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12022859	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12024941	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12026367	0.95[AFR][1000 genomes]
rs12027548	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12031606	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12036085	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12038745	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12039546	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12042509	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12046536	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12093742	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12562103	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12563826	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360365	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1576592	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1611832	0.94[EUR][1000 genomes]
rs1622451	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623248	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1623314	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1629275	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1687947	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1687950	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17111408	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17111419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17111426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17111436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1765636	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1765640	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1929131	0.87[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1999270	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1999271	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2130899	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391472	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35275815	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3789690	0.83[EUR][1000 genomes]
rs4543802	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4847201	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4847296	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55961421	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56037795	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57666908	0.83[EUR][1000 genomes]
rs6541343	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6541345	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6662877	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6673491	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6675959	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6681827	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66918029	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66961454	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67180557	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67554381	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67612304	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67681803	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67807923	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs68193246	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7413345	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7415246	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515965	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7520754	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7525320	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7533977	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7554714	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94788600-94800800	Weak transcription	Pancreas	Pancrea
2	chr1:94792400-94800200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:94793200-94800600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:94796000-94800200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr1:94796000-94800400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:94796000-94800600	Weak transcription	Adipose Nuclei	Adipose
7	chr1:94796000-94800600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:94796000-94804600	Weak transcription	Fetal Thymus	thymus
9	chr1:94796000-94804800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:94796000-94807800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:94796200-94800400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:94796400-94800200	Weak transcription	Left Ventricle	heart
13	chr1:94796600-94804800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:94798200-94801400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:94798200-94802000	Enhancers	Osteobl	bone
16	chr1:94798200-94802400	Enhancers	Muscle Satellite Cultured Cells	--
17	chr1:94798400-94801000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:94798400-94801000	Enhancers	HSMMtube	muscle
19	chr1:94798400-94801200	Enhancers	A549	lung
20	chr1:94798400-94801200	Enhancers	HSMM	muscle
21	chr1:94798400-94801400	Enhancers	HMEC	breast
22	chr1:94798600-94800200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:94798600-94801200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:94798600-94801200	Enhancers	NHLF	lung
25	chr1:94798800-94801000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:94798800-94801000	Enhancers	Placenta	Placenta
27	chr1:94798800-94801000	Enhancers	Fetal Stomach	stomach
28	chr1:94799000-94800200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:94799000-94800200	Weak transcription	Fetal Kidney	kidney
30	chr1:94799000-94800400	Enhancers	GM12878-XiMat	blood
31	chr1:94799000-94800800	Weak transcription	HUVEC	blood vessel
32	chr1:94799000-94805200	Weak transcription	Lung	lung
33	chr1:94799200-94800200	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:94799200-94800200	Weak transcription	Fetal Heart	heart
35	chr1:94799200-94800200	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr1:94799200-94800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:94799200-94801200	Weak transcription	NHEK	skin
38	chr1:94799200-94812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:94799800-94800400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:94799800-94800400	Enhancers	Fetal Muscle Leg	muscle
41	chr1:94799800-94800800	Enhancers	NH-A	brain
42	chr1:94799800-94801000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:94800000-94801000	Enhancers	HepG2	liver
44	chr1:94800000-94801000	Enhancers	NHDF-Ad	bronchial
45	chr1:94800000-94801200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:94800000-94804800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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