Variant report

Variant	rs3820541
Chromosome Location	chr1:150848681-150848682
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150549744..150554023-chr1:150847608..150851573,5	K562	blood:
2	chr1:150847503..150849791-chr1:150897618..150900781,3	K562	blood:
3	chr1:150847931..150851587-chr1:150853004..150856091,6	K562	blood:
4	chr1:150847223..150849804-chr14:20928193..20929999,2	MCF-7	breast:
5	chr1:150830646..150832634-chr1:150847170..150848850,2	MCF-7	breast:
6	chr1:150847356..150848927-chr1:150849575..150851202,2	K562	blood:
7	chr1:150846965..150851829-chr1:150851958..150856513,6	MCF-7	breast:
8	chr1:150549206..150551464-chr1:150847559..150850045,2	K562	blood:
9	chr1:150533798..150536086-chr1:150845330..150849365,4	MCF-7	breast:
10	chr1:150848210..150848854-chr1:150951690..150952505,2	K562	blood:
11	chr1:150847731..150849909-chr1:150942826..150945486,2	K562	blood:
12	chr1:150847391..150850807-chr1:150896212..150900555,5	MCF-7	breast:
13	chr1:150847696..150850504-chr1:150946094..150948149,2	K562	blood:
14	chr1:150846616..150850276-chr1:150942456..150948926,7	MCF-7	breast:
15	chr1:150846958..150850554-chr1:150897225..150899118,3	K562	blood:
16	chr1:150848386..150850942-chr1:150853921..150858032,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000231073	Chromatin interaction
ENSG00000165782	Chromatin interaction
ENSG00000143418	Chromatin interaction
ENSG00000224800	Chromatin interaction
ENSG00000143379	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000203804	Chromatin interaction
ENSG00000212512	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10788795	0.88[EUR][1000 genomes]
rs10888396	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204714	0.85[EUR][1000 genomes]
rs11204715	0.85[EUR][1000 genomes]
rs11204727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11576175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12728254	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16832604	0.91[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs16840074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1811698	0.81[ASN][1000 genomes]
rs2134688	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs267736	0.91[CEU][hapmap]
rs3738483	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3754210	0.91[CEU][hapmap]
rs3768017	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820543	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4379678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs533928	0.91[EUR][1000 genomes]
rs61817598	0.82[EUR][1000 genomes]
rs61817600	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61817649	0.91[EUR][1000 genomes]
rs6661100	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6671703	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6679701	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6684611	0.93[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6688248	0.91[EUR][1000 genomes]
rs6692277	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6696167	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72704624	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7517566	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7529204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535848	0.91[EUR][1000 genomes]
rs7535975	0.85[EUR][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	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv2810	chr1:150835173-150879869	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1008496	chr1:150845827-150970656	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150846600-150849200	Active TSS	Ovary	ovary
2	chr1:150846600-150850000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:150846600-150850000	Active TSS	Aorta	Aorta
4	chr1:150846600-150850000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr1:150846800-150848800	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr1:150846800-150849200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:150846800-150849200	Active TSS	NHDF-Ad	bronchial
8	chr1:150846800-150849800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:150847000-150849800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:150847000-150850200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:150847200-150849600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:150847200-150849600	Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr1:150847200-150849800	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr1:150847200-150849800	Active TSS	Psoas Muscle	Psoas
15	chr1:150847200-150849800	Active TSS	Right Atrium	heart
16	chr1:150847200-150849800	Active TSS	Right Ventricle	heart
17	chr1:150847200-150849800	Active TSS	HSMM	muscle
18	chr1:150847400-150849200	Active TSS	NHLF	lung
19	chr1:150847400-150849600	Active TSS	Placenta	Placenta
20	chr1:150847400-150849600	Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr1:150847400-150849800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:150847400-150849800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:150847400-150849800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:150847400-150849800	Active TSS	Fetal Muscle Leg	muscle
25	chr1:150847400-150849800	Active TSS	Thymus	Thymus
26	chr1:150847400-150849800	Active TSS	HepG2	liver
27	chr1:150847400-150849800	Active TSS	HSMMtube	muscle
28	chr1:150847400-150850000	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr1:150847400-150850000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:150847400-150850000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:150847400-150850000	Active TSS	Brain Anterior Caudate	brain
32	chr1:150847400-150850000	Active TSS	Rectal Smooth Muscle	rectum
33	chr1:150847400-150850000	Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr1:150847400-150850000	Active TSS	Stomach Smooth Muscle	stomach
35	chr1:150847400-150850200	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr1:150847400-150850200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:150847600-150849600	Active TSS	Osteobl	bone
38	chr1:150847600-150849800	Active TSS	Brain Angular Gyrus	brain
39	chr1:150847600-150849800	Active TSS	Brain Germinal Matrix	brain
40	chr1:150847600-150849800	Active TSS	Colon Smooth Muscle	Colon
41	chr1:150847600-150849800	Active TSS	Fetal Brain Male	brain
42	chr1:150847600-150849800	Active TSS	Fetal Lung	lung
43	chr1:150847600-150849800	Active TSS	Fetal Stomach	stomach
44	chr1:150847600-150849800	Active TSS	NH-A	brain
45	chr1:150847600-150850000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr1:150847600-150850000	Active TSS	Muscle Satellite Cultured Cells	--
47	chr1:150847600-150850000	Active TSS	GM12878-XiMat	blood
48	chr1:150847600-150850000	Active TSS	HMEC	breast
49	chr1:150847600-150850200	Active TSS	A549	lung
50	chr1:150847800-150849200	Active TSS	Fetal Thymus	thymus

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