Variant report

Variant	rs225627
Chromosome Location	chr6:142472366-142472367
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	chr6:142470687..142472679-chr6:142481549..142483699,2	K562	blood:
3	chr6:142472276..142475078-chr6:142622089..142623666,2	MCF-7	breast:
4	chr6:142469818..142472806-chr6:142621459..142623184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000009844	Chromatin interaction
ENSG00000112414	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11155234	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs1342059	1.00[JPT][hapmap]
rs225625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225646	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs225711	1.00[JPT][hapmap]
rs225712	0.82[EUR][1000 genomes]
rs225714	0.81[EUR][1000 genomes]
rs225715	0.82[EUR][1000 genomes]
rs225716	0.82[EUR][1000 genomes]
rs225717	0.82[EUR][1000 genomes]
rs225718	0.82[EUR][1000 genomes]
rs225719	0.81[EUR][1000 genomes]
rs225726	0.81[EUR][1000 genomes]
rs225727	0.81[EUR][1000 genomes]
rs225729	0.81[EUR][1000 genomes]
rs225730	0.81[EUR][1000 genomes]
rs225731	0.81[EUR][1000 genomes]
rs225732	0.81[EUR][1000 genomes]
rs225733	0.81[EUR][1000 genomes]
rs225737	0.81[EUR][1000 genomes]
rs225738	0.81[EUR][1000 genomes]
rs225740	0.81[EUR][1000 genomes]
rs225741	0.81[EUR][1000 genomes]
rs225743	0.81[EUR][1000 genomes]
rs225745	0.81[EUR][1000 genomes]
rs225746	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:99 , 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	chr6:142469800-142472600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr6:142469800-142481200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:142469800-142487600	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr6:142470000-142476600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:142470000-142477000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:142470000-142477200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr6:142470000-142481400	Weak transcription	Gastric	stomach
14	chr6:142470000-142484000	Weak transcription	Psoas Muscle	Psoas
15	chr6:142470000-142486400	Weak transcription	Fetal Intestine Small	intestine
16	chr6:142470200-142474000	Weak transcription	NH-A	brain
17	chr6:142470200-142484000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:142470200-142487800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:142470200-142488200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr6:142470200-142488200	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
22	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
23	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
24	chr6:142470400-142473400	Weak transcription	Osteobl	bone
25	chr6:142470400-142473800	Weak transcription	A549	lung
26	chr6:142470400-142473800	Weak transcription	Hela-S3	cervix
27	chr6:142470400-142473800	Weak transcription	NHEK	skin
28	chr6:142470400-142473800	Weak transcription	NHLF	lung
29	chr6:142470400-142474000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr6:142470400-142476200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr6:142470400-142476600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:142470400-142476800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr6:142470400-142476800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr6:142470400-142477000	Weak transcription	Adipose Nuclei	Adipose
35	chr6:142470400-142477000	Weak transcription	Brain Substantia Nigra	brain
36	chr6:142470400-142477000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr6:142470400-142477000	Weak transcription	HSMM	muscle
38	chr6:142470400-142487400	Weak transcription	Duodenum Mucosa	Duodenum
39	chr6:142470400-142487600	Weak transcription	Primary monocytes fromperipheralblood	blood
40	chr6:142470400-142487600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr6:142470400-142487600	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr6:142470600-142472400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:142470600-142472400	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:142470600-142473200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:142470600-142473200	Weak transcription	NHDF-Ad	bronchial
46	chr6:142470600-142474000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr6:142470600-142475000	Weak transcription	Fetal Brain Male	brain
48	chr6:142470600-142476000	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr6:142470600-142476800	Weak transcription	K562	blood
50	chr6:142470600-142477000	Weak transcription	H1 Cell Line	embryonic stem cell

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