Variant report

Variant	rs1890544
Chromosome Location	chr6:128648951-128648952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:128647886..128650591-chr6:128840783..128842601,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1339190	0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1339195	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1556886	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1738272	0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs2326681	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4897254	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs6914789	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs6922127	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73596689	0.85[AFR][1000 genomes]
rs7738641	0.93[YRI][hapmap];0.94[AFR][1000 genomes]
rs7742250	0.86[YRI][hapmap];0.94[AFR][1000 genomes]
rs7745739	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7774819	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs9388630	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9402034	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][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	nsv1033443	chr6:128306654-128899203	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv538440	chr6:128306654-128899203	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886649	chr6:128399657-128808054	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128621800-128649000	Weak transcription	HSMMtube	muscle
2	chr6:128627800-128649000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:128631800-128649000	Weak transcription	Aorta	Aorta
4	chr6:128632000-128649000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:128632000-128650600	Weak transcription	Psoas Muscle	Psoas
6	chr6:128632000-128650800	Weak transcription	Right Ventricle	heart
7	chr6:128632000-128658000	Weak transcription	Ovary	ovary
8	chr6:128632200-128665200	Weak transcription	Gastric	stomach
9	chr6:128633600-128649000	Weak transcription	Fetal Thymus	thymus
10	chr6:128635600-128672000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr6:128635800-128654200	Weak transcription	Liver	Liver
12	chr6:128639000-128660600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr6:128639000-128660800	Weak transcription	Small Intestine	intestine
14	chr6:128639800-128659000	Weak transcription	Fetal Stomach	stomach
15	chr6:128640000-128653200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:128640000-128660600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:128640600-128649000	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr6:128640600-128649000	Weak transcription	Primary T cells from cord blood	blood
19	chr6:128641400-128649000	Weak transcription	Fetal Lung	lung
20	chr6:128641400-128661400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:128641800-128657600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr6:128642000-128649000	Weak transcription	Left Ventricle	heart
23	chr6:128642000-128657000	Weak transcription	HepG2	liver
24	chr6:128643400-128649000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:128643400-128649000	Weak transcription	HSMM	muscle
26	chr6:128643400-128659000	Weak transcription	NHEK	skin
27	chr6:128643400-128660600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:128643600-128653400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:128645000-128654800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr6:128646200-128657000	Weak transcription	Brain Anterior Caudate	brain
31	chr6:128648200-128650600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr6:128648600-128649400	ZNF genes & repeats	Fetal Intestine Large	intestine
33	chr6:128648600-128649400	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr6:128648800-128649400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr6:128648800-128654400	Weak transcription	A549	lung

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