Variant report

Variant	rs7178244
Chromosome Location	chr15:41008153-41008154
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	chr15:41006871..41009134-chr15:41015963..41018302,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM82A2-1	chr15:41006211-41008592	ENSG00000245312

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10220885	1.00[EUR][1000 genomes]
rs12323939	1.00[EUR][1000 genomes]
rs16971119	1.00[EUR][1000 genomes]
rs45501094	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45571032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45604436	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55896567	1.00[EUR][1000 genomes]
rs55906732	1.00[EUR][1000 genomes]
rs56229816	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57242620	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57288992	1.00[EUR][1000 genomes]
rs58097169	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58375351	1.00[EUR][1000 genomes]
rs58681580	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58738238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59508492	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59528823	1.00[EUR][1000 genomes]
rs59558714	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60109064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60111609	1.00[EUR][1000 genomes]
rs60163307	1.00[EUR][1000 genomes]
rs60578270	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60822673	1.00[EUR][1000 genomes]
rs6492962	0.89[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6492963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7161941	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7164574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7166733	1.00[EUR][1000 genomes]
rs7167831	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7168217	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7169273	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7171451	1.00[ASW][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171898	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7172356	0.85[LWK][hapmap];0.83[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178058	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs7182066	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7182516	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011880	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011881	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011884	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011886	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74011887	1.00[EUR][1000 genomes]
rs74011888	1.00[EUR][1000 genomes]
rs74011933	1.00[EUR][1000 genomes]
rs74011936	1.00[EUR][1000 genomes]
rs8025846	0.85[YRI][hapmap]
rs8035580	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8038751	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8039169	1.00[EUR][1000 genomes]
rs8039942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8040579	1.00[EUR][1000 genomes]
rs8040925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9672224	1.00[EUR][1000 genomes]
rs9744142	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	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
4	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
8	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
12	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
13	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
15	chr15:40989000-41012000	Weak transcription	NHLF	lung
16	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:40990200-41013200	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr15:40990200-41016800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:40990200-41016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:40990600-41015000	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:40990800-41016000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:40992000-41016600	Strong transcription	Dnd41	blood
24	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr15:40994000-41020600	Weak transcription	HSMM	muscle
26	chr15:40997800-41020800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr15:40998200-41023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
29	chr15:40999000-41011600	Weak transcription	Fetal Intestine Large	intestine
30	chr15:40999000-41027600	Weak transcription	Gastric	stomach
31	chr15:40999200-41021600	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:41001000-41008400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr15:41001400-41020800	Weak transcription	NHDF-Ad	bronchial
35	chr15:41001600-41020600	Weak transcription	NH-A	brain
36	chr15:41002000-41019600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:41002000-41021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:41002200-41011000	Weak transcription	Fetal Intestine Small	intestine
39	chr15:41002200-41021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr15:41002400-41009000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:41002800-41008600	Strong transcription	GM12878-XiMat	blood
42	chr15:41002800-41019400	Weak transcription	Fetal Stomach	stomach
43	chr15:41003200-41021800	Weak transcription	Brain Germinal Matrix	brain
44	chr15:41003400-41010200	Weak transcription	Thymus	Thymus
45	chr15:41003600-41010800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:41003600-41013800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:41003600-41021800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:41003800-41015600	Weak transcription	HMEC	breast
49	chr15:41003800-41023800	Weak transcription	Fetal Lung	lung
50	chr15:41004000-41021600	Weak transcription	Osteobl	bone

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