Variant report

Variant	rs12664858
Chromosome Location	chr6:151075238-151075239
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:151074081..151075866-chr6:151078456..151080044,2	MCF-7	breast:
2	chr6:151073651..151077490-chr6:151086273..151089717,3	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs12662499	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12663819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664005	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13196740	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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13201828	1.00[ASN][1000 genomes]
rs13201855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211397	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13211603	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13216327	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17080241	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs17340521	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs34254299	0.84[EUR][1000 genomes]
rs4645433	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028508	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57798861	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71570234	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71570235	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7453338	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9478809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997374	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030326	chr6:150967665-151641372	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019919	chr6:151028969-151161789	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv538474	chr6:151028969-151161789	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:151042600-151085400	Weak transcription	Esophagus	oesophagus
2	chr6:151056000-151087200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:151058600-151075600	Weak transcription	Thymus	Thymus
4	chr6:151061600-151112200	Weak transcription	Right Atrium	heart
5	chr6:151072000-151075400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:151072400-151079400	Strong transcription	Primary B cells from cord blood	blood
7	chr6:151072800-151077200	Weak transcription	HUVEC	blood vessel
8	chr6:151072800-151085600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:151073600-151078000	Enhancers	Fetal Muscle Leg	muscle
10	chr6:151073800-151076600	Weak transcription	Fetal Thymus	thymus
11	chr6:151074000-151076200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr6:151074400-151075400	Enhancers	Fetal Muscle Trunk	muscle
13	chr6:151074400-151075600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:151074400-151075600	Enhancers	Placenta Amnion	Placenta Amnion
15	chr6:151074400-151076600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr6:151074600-151075400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:151074600-151075400	Enhancers	Brain Hippocampus Middle	brain
18	chr6:151074600-151075400	Flanking Active TSS	Fetal Heart	heart
19	chr6:151074600-151075400	Enhancers	Ovary	ovary
20	chr6:151074600-151075600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr6:151074600-151076000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:151074600-151077600	Enhancers	Left Ventricle	heart
23	chr6:151074600-151078000	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr6:151074800-151075400	Enhancers	H9 Cell Line	embryonic stem cell
25	chr6:151074800-151075400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:151074800-151075400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
27	chr6:151074800-151075400	Enhancers	Spleen	Spleen
28	chr6:151074800-151075600	Bivalent Enhancer	Fetal Intestine Small	intestine
29	chr6:151074800-151075800	Enhancers	Adipose Nuclei	Adipose
30	chr6:151075000-151075400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr6:151075000-151075400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
32	chr6:151075000-151075400	Bivalent Enhancer	Brain Anterior Caudate	brain
33	chr6:151075000-151075400	Enhancers	Fetal Stomach	stomach
34	chr6:151075000-151075400	Enhancers	Rectal Smooth Muscle	rectum
35	chr6:151075000-151075400	Enhancers	HMEC	breast
36	chr6:151075000-151075600	Enhancers	Brain Germinal Matrix	brain
37	chr6:151075000-151075600	Enhancers	Fetal Kidney	kidney
38	chr6:151075000-151075600	Bivalent Enhancer	HSMMtube	muscle
39	chr6:151075000-151075800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:151075000-151076800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:151075000-151077400	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr6:151075000-151077400	Enhancers	Lung	lung
43	chr6:151075000-151078000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr6:151075000-151078000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr6:151075200-151075600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr6:151075200-151075600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr6:151075200-151075600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr6:151075200-151075600	Enhancers	Brain Cingulate Gyrus	brain
49	chr6:151075200-151075600	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr6:151075200-151075600	Bivalent Enhancer	Fetal Brain Male	brain

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