Variant report

Variant	rs9462384
Chromosome Location	chr6:38100104-38100105
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	chr6:38099507..38102377-chr6:38107497..38109625,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11759344	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11961284	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13437101	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55749139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55890079	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55933649	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57327758	0.98[AFR][1000 genomes]
rs57953063	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57965615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58860274	0.82[AFR][1000 genomes]
rs60249007	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60774419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60997161	0.85[AFR][1000 genomes]
rs6904932	0.89[YRI][hapmap];0.85[AFR][1000 genomes]
rs6917912	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6918181	0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs6918445	0.89[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6918779	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6919188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6924117	0.89[YRI][hapmap]
rs6941852	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73730849	0.82[AFR][1000 genomes]
rs73730859	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs73730865	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73730881	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73730883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73730892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73730893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73730896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73730897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73734310	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73734311	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73734320	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7747924	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7767077	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7770297	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7773080	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9296235	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9462381	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462382	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9462383	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462385	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462386	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9462388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9462390	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470731	0.88[YRI][hapmap]
rs9470736	0.88[YRI][hapmap]
rs9470744	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs9470745	0.84[AFR][1000 genomes]
rs9470746	1.00[EUR][1000 genomes]
rs9470757	0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470766	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470770	0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470771	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470774	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470781	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470783	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470786	0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470789	1.00[YRI][hapmap]
rs9470790	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470792	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470795	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470797	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9470799	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1020625	chr6:37833591-38155622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2754649	chr6:37985025-38147910	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38045600-38107000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr6:38057200-38109200	Weak transcription	K562	blood
3	chr6:38060000-38108200	Weak transcription	Ovary	ovary
4	chr6:38072200-38108400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:38075200-38118200	Weak transcription	Colonic Mucosa	Colon
6	chr6:38075400-38103800	Weak transcription	Pancreas	Pancrea
7	chr6:38076600-38104000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:38078800-38109000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:38078800-38111000	Weak transcription	Fetal Kidney	kidney
10	chr6:38078800-38111000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:38079600-38113800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:38080400-38104800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr6:38081800-38121800	Weak transcription	Psoas Muscle	Psoas
14	chr6:38083800-38103800	Weak transcription	Esophagus	oesophagus
15	chr6:38084000-38122200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr6:38084600-38124200	Weak transcription	Hela-S3	cervix
17	chr6:38086600-38102400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:38087200-38101600	Weak transcription	Brain Angular Gyrus	brain
19	chr6:38087600-38100400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr6:38087600-38101800	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:38087600-38103800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:38087600-38104800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:38087600-38118800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:38087800-38104600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr6:38088000-38102200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:38088000-38104800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:38089200-38103800	Weak transcription	Gastric	stomach
28	chr6:38089600-38106200	Weak transcription	Placenta	Placenta
29	chr6:38090000-38111000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr6:38090400-38106200	Weak transcription	NHEK	skin
31	chr6:38091200-38106200	Weak transcription	Dnd41	blood
32	chr6:38091200-38119800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr6:38091400-38100400	Weak transcription	HepG2	liver
34	chr6:38091400-38109400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:38091400-38110200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:38091400-38110400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:38091400-38116000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:38091400-38141800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr6:38091600-38101000	Weak transcription	Primary B cells from peripheral blood	blood
40	chr6:38091800-38107200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:38091800-38109600	Weak transcription	Fetal Muscle Trunk	muscle
42	chr6:38092000-38100400	Weak transcription	Fetal Thymus	thymus
43	chr6:38092000-38102600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:38092200-38100600	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr6:38092400-38100400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:38092600-38100400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:38092600-38100400	Weak transcription	Fetal Stomach	stomach
48	chr6:38092600-38102400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr6:38092600-38104000	Weak transcription	Thymus	Thymus
50	chr6:38092600-38109000	Weak transcription	Lung	lung

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