Variant report

Variant	rs620905
Chromosome Location	chr1:241791957-241791958
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:241791375..241793917-chr1:241997921..242000240,2	MCF-7	breast:
2	chr1:241692639..241698024-chr1:241788169..241793747,6	K562	blood:
3	chr1:241745713..241748645-chr1:241790250..241792527,2	K562	blood:
4	chr1:241697913..241700856-chr1:241791206..241793471,2	MCF-7	breast:
5	chr1:241693845..241695449-chr1:241789747..241792486,2	MCF-7	breast:
6	chr1:241787560..241792499-chr1:241801954..241804865,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117009	Chromatin interaction
ENSG00000054277	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs606004	1.00[AMR][1000 genomes]
rs637280	0.99[AFR][1000 genomes]
rs642902	1.00[AMR][1000 genomes]
rs655327	0.95[LWK][hapmap];0.91[MKK][hapmap];1.00[AMR][1000 genomes]
rs669785	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes]
rs684377	1.00[AMR][1000 genomes]
rs684742	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv918034	chr1:241072791-242005532	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
2	nsv997966	chr1:241100739-242087629	Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1002214	chr1:241458939-242099790	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
4	nsv549460	chr1:241494578-241833287	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1009579	chr1:241499537-241824631	Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv530112	chr1:241522031-241840269	Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv873368	chr1:241533392-242195928	Weak transcription Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv873372	chr1:241690554-242438293	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	nsv427963	chr1:241718799-241832833	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:241758000-241797200	Weak transcription	Left Ventricle	heart
2	chr1:241758000-241800200	Weak transcription	Ovary	ovary
3	chr1:241758800-241802400	Weak transcription	Right Ventricle	heart
4	chr1:241766200-241798600	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:241776400-241795000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr1:241776400-241795200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:241776400-241795800	Weak transcription	Hela-S3	cervix
8	chr1:241776400-241797400	Weak transcription	NHLF	lung
9	chr1:241779400-241798600	Weak transcription	Fetal Intestine Large	intestine
10	chr1:241779400-241800400	Weak transcription	Osteobl	bone
11	chr1:241779400-241800600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:241779400-241801000	Weak transcription	Fetal Intestine Small	intestine
13	chr1:241779600-241796600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:241779800-241795200	Weak transcription	Placenta	Placenta
15	chr1:241781200-241799800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:241783400-241798000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:241784400-241800600	Weak transcription	Fetal Brain Male	brain
18	chr1:241785200-241798800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:241785400-241797200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:241786200-241800400	Weak transcription	Psoas Muscle	Psoas
21	chr1:241786600-241800800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr1:241786800-241796200	Weak transcription	Fetal Brain Female	brain
23	chr1:241787600-241797200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:241787800-241802400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr1:241788000-241792000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:241788200-241800800	Weak transcription	Gastric	stomach
27	chr1:241788200-241801400	Weak transcription	Colonic Mucosa	Colon
28	chr1:241788200-241802800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:241788200-241802800	Weak transcription	Esophagus	oesophagus
30	chr1:241788800-241797800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:241788800-241797800	Weak transcription	Duodenum Mucosa	Duodenum
32	chr1:241789200-241797800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:241789200-241802800	Weak transcription	Pancreas	Pancrea
34	chr1:241789800-241796400	Weak transcription	Dnd41	blood
35	chr1:241790600-241792400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:241790600-241793000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:241790800-241792000	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr1:241791000-241792000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:241791000-241792000	Genic enhancers	A549	lung
40	chr1:241791000-241793800	Weak transcription	Fetal Lung	lung
41	chr1:241791000-241797400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:241791000-241797400	Weak transcription	NH-A	brain
43	chr1:241791000-241799600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:241791200-241792000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr1:241791200-241792000	Strong transcription	HSMMtube	muscle
46	chr1:241791400-241792000	Strong transcription	Brain Germinal Matrix	brain
47	chr1:241791400-241792000	Strong transcription	HSMM	muscle
48	chr1:241791400-241793200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:241791400-241795400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:241791400-241797600	Weak transcription	NHEK	skin

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