Variant report

Variant	rs4897254
Chromosome Location	chr6:128675291-128675292
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	chr6:128668869..128672151-chr6:128674907..128677804,3	MCF-7	breast:
2	chr6:128670739..128672658-chr6:128673708..128675323,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1339190	0.86[YRI][hapmap];0.90[AFR][1000 genomes]
rs1339192	0.90[AFR][1000 genomes]
rs1339194	0.90[AFR][1000 genomes]
rs1339195	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs1556886	0.92[YRI][hapmap];0.92[AFR][1000 genomes]
rs1738272	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1738295	1.00[AMR][1000 genomes]
rs1890544	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs2326681	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs4351279	0.86[YRI][hapmap]
rs6914789	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs6922127	0.90[AFR][1000 genomes]
rs7738641	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7742250	0.92[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7745739	1.00[ASW][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs7774819	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs8180639	0.86[YRI][hapmap]
rs9388630	0.92[YRI][hapmap];0.94[AFR][1000 genomes]
rs9402034	0.92[YRI][hapmap];0.90[AFR][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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128649400-128678600	Weak transcription	HSMM	muscle
2	chr6:128661400-128677200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:128661600-128679400	Weak transcription	Osteobl	bone
4	chr6:128666000-128678600	Weak transcription	Left Ventricle	heart
5	chr6:128666000-128679400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:128668400-128677200	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr6:128668600-128677200	Weak transcription	Small Intestine	intestine
8	chr6:128668600-128684200	Weak transcription	Fetal Kidney	kidney
9	chr6:128670400-128677400	Weak transcription	HSMMtube	muscle
10	chr6:128670400-128678600	Weak transcription	Brain Angular Gyrus	brain
11	chr6:128670400-128678600	Weak transcription	Brain Substantia Nigra	brain
12	chr6:128670600-128678000	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:128671800-128678000	Weak transcription	Right Ventricle	heart
14	chr6:128672200-128675800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:128672200-128678200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:128672400-128675800	Weak transcription	Colon Smooth Muscle	Colon
17	chr6:128672400-128675800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr6:128673000-128679000	Weak transcription	NH-A	brain
19	chr6:128673000-128681000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr6:128673000-128687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:128673200-128683200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:128674000-128675800	Weak transcription	Fetal Intestine Small	intestine
23	chr6:128674000-128684200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:128674000-128685800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr6:128674200-128679400	Weak transcription	Stomach Mucosa	stomach
26	chr6:128674400-128675800	Weak transcription	Fetal Lung	lung
27	chr6:128674600-128679400	Weak transcription	HepG2	liver
28	chr6:128674800-128676200	Enhancers	Fetal Intestine Large	intestine
29	chr6:128674800-128677600	Weak transcription	Fetal Heart	heart
30	chr6:128675000-128688000	Weak transcription	Gastric	stomach

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