Variant report

Variant	rs225628
Chromosome Location	chr6:142472936-142472937
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:142467284..142470196-chr6:142471245..142474194,3	MCF-7	breast:
2	chr6:142472276..142475078-chr6:142622089..142623666,2	MCF-7	breast:
3	chr6:142467354..142470358-chr6:142472632..142476145,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112414	Chromatin interaction
ENSG00000009844	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs225601	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225602	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225606	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225618	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225622	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225623	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225624	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225629	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225630	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225631	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225632	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225633	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225634	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225635	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225636	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225637	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225639	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225640	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225641	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225642	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225643	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225650	0.91[EUR][1000 genomes]
rs225651	0.91[EUR][1000 genomes]
rs225652	0.91[EUR][1000 genomes]
rs225653	0.91[EUR][1000 genomes]
rs225654	0.91[EUR][1000 genomes]
rs225655	0.91[EUR][1000 genomes]
rs225656	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs225657	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs225658	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs225659	0.91[EUR][1000 genomes]
rs225660	0.90[EUR][1000 genomes]
rs225661	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs225662	0.91[EUR][1000 genomes]
rs225663	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs225664	0.87[EUR][1000 genomes]
rs225665	0.88[EUR][1000 genomes]
rs225671	0.82[AMR][1000 genomes]
rs225688	0.92[ASN][1000 genomes]
rs62430473	0.82[ASN][1000 genomes]
rs628311	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs639658	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6939944	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939975	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][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	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	esv3334782	chr6:142472872-142473065	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142468800-142488000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:142469200-142477000	Weak transcription	Stomach Mucosa	stomach
3	chr6:142469200-142483400	Weak transcription	Aorta	Aorta
4	chr6:142469200-142487800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr6:142469600-142487800	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:142469600-142487800	Weak transcription	Thymus	Thymus
7	chr6:142469800-142481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:142469800-142487600	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr6:142470000-142476600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr6:142470000-142477000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr6:142470000-142477200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr6:142470000-142481400	Weak transcription	Gastric	stomach
13	chr6:142470000-142484000	Weak transcription	Psoas Muscle	Psoas
14	chr6:142470000-142486400	Weak transcription	Fetal Intestine Small	intestine
15	chr6:142470200-142474000	Weak transcription	NH-A	brain
16	chr6:142470200-142484000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr6:142470200-142487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:142470200-142488200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr6:142470200-142488200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
21	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
22	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
23	chr6:142470400-142473400	Weak transcription	Osteobl	bone
24	chr6:142470400-142473800	Weak transcription	A549	lung
25	chr6:142470400-142473800	Weak transcription	Hela-S3	cervix
26	chr6:142470400-142473800	Weak transcription	NHEK	skin
27	chr6:142470400-142473800	Weak transcription	NHLF	lung
28	chr6:142470400-142474000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:142470400-142476200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:142470400-142476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:142470400-142476800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:142470400-142476800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:142470400-142477000	Weak transcription	Adipose Nuclei	Adipose
34	chr6:142470400-142477000	Weak transcription	Brain Substantia Nigra	brain
35	chr6:142470400-142477000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr6:142470400-142477000	Weak transcription	HSMM	muscle
37	chr6:142470400-142487400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr6:142470400-142487600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr6:142470400-142487600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:142470400-142487600	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:142470600-142473200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:142470600-142473200	Weak transcription	NHDF-Ad	bronchial
43	chr6:142470600-142474000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr6:142470600-142475000	Weak transcription	Fetal Brain Male	brain
45	chr6:142470600-142476000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr6:142470600-142476800	Weak transcription	K562	blood
47	chr6:142470600-142477000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:142470600-142477000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:142470600-142477200	Weak transcription	Small Intestine	intestine
50	chr6:142470600-142483800	Weak transcription	Fetal Lung	lung

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