Variant report

Variant	rs12524527
Chromosome Location	chr6:16647646-16647647
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	chr6:16647525..16649977-chr6:16668456..16671117,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10949371	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10949372	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12198838	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211723	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17603856	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17667167	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs2143067	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62387972	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532022	chr6:16448152-16825567	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1031423	chr6:16467215-16823725	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1015992	chr6:16469059-16846847	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers 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	17 gene(s)	inside rSNPs	diseases
4	nsv538148	chr6:16469059-16846847	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:16584000-16670000	Weak transcription	Fetal Brain Male	brain
2	chr6:16606000-16653200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr6:16622200-16651400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr6:16626200-16654000	Weak transcription	Fetal Kidney	kidney
5	chr6:16627800-16652000	Weak transcription	Thymus	Thymus
6	chr6:16629000-16653400	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr6:16632000-16652000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr6:16634400-16651400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:16634400-16653200	Weak transcription	Fetal Heart	heart
10	chr6:16634600-16648200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr6:16636400-16653400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:16636800-16650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr6:16636800-16651400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr6:16636800-16652000	Weak transcription	Aorta	Aorta
15	chr6:16636800-16652200	Weak transcription	Psoas Muscle	Psoas
16	chr6:16636800-16652800	Weak transcription	Esophagus	oesophagus
17	chr6:16636800-16652800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr6:16636800-16653400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:16636800-16653400	Weak transcription	Left Ventricle	heart
20	chr6:16636800-16653400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr6:16636800-16653400	Weak transcription	Spleen	Spleen
22	chr6:16636800-16653600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr6:16636800-16658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:16636800-16661800	Weak transcription	Right Ventricle	heart
25	chr6:16636800-16667400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr6:16636800-16669400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:16636800-16672600	Weak transcription	Gastric	stomach
28	chr6:16637000-16648400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:16637000-16649800	Weak transcription	A549	lung
30	chr6:16637000-16658800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:16639800-16651800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:16640000-16659800	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr6:16640200-16661600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:16640400-16661800	Weak transcription	NHLF	lung
35	chr6:16640600-16651800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr6:16640600-16651800	Weak transcription	HMEC	breast
37	chr6:16640600-16651800	Weak transcription	HSMMtube	muscle
38	chr6:16640600-16655000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr6:16640600-16656800	Weak transcription	Brain Angular Gyrus	brain
40	chr6:16640600-16659000	Weak transcription	Hela-S3	cervix
41	chr6:16640800-16649400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:16640800-16650400	Weak transcription	HSMM	muscle
43	chr6:16640800-16656400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr6:16641200-16651800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr6:16641200-16651800	Weak transcription	NHEK	skin
46	chr6:16641200-16653600	Weak transcription	Placenta	Placenta
47	chr6:16641200-16653600	Weak transcription	NH-A	brain
48	chr6:16641400-16651800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr6:16641400-16658800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr6:16641800-16650000	Weak transcription	Brain Anterior Caudate	brain

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