Variant report

Variant	rs74088338
Chromosome Location	chr12:39696197-39696198
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39690972..39693239-chr12:39694761..39697625,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1913189	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55756650	1.00[AMR][1000 genomes]
rs56114183	1.00[AMR][1000 genomes]
rs56224231	1.00[AMR][1000 genomes]
rs57847806	1.00[AMR][1000 genomes]
rs58046207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58297221	1.00[AMR][1000 genomes]
rs74086512	1.00[AMR][1000 genomes]
rs74086516	1.00[AMR][1000 genomes]
rs74086528	1.00[AMR][1000 genomes]
rs74086539	1.00[AMR][1000 genomes]
rs74086540	1.00[AMR][1000 genomes]
rs74086548	1.00[AMR][1000 genomes]
rs74086549	1.00[AMR][1000 genomes]
rs74086569	1.00[AMR][1000 genomes]
rs74088332	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088334	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088343	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088350	1.00[AMR][1000 genomes]
rs74088351	1.00[AMR][1000 genomes]
rs74088356	1.00[AMR][1000 genomes]
rs74088360	1.00[AMR][1000 genomes]
rs74088362	1.00[AMR][1000 genomes]
rs74088365	1.00[AMR][1000 genomes]
rs74088368	1.00[AMR][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	nsv899013	chr12:39567945-39732430	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv470286	chr12:39651893-39729700	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv558589	chr12:39667861-39768356	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39682000-39699200	Weak transcription	Hela-S3	cervix
2	chr12:39685200-39697400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr12:39685200-39714400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr12:39686400-39699600	Weak transcription	HMEC	breast
5	chr12:39686600-39722400	Weak transcription	GM12878-XiMat	blood
6	chr12:39686600-39725400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:39686800-39729800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:39686800-39738800	Weak transcription	Pancreas	Pancrea
9	chr12:39687200-39696800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:39687200-39726400	Weak transcription	Fetal Intestine Small	intestine
11	chr12:39687600-39723800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr12:39688400-39709800	Weak transcription	Ovary	ovary
13	chr12:39688400-39724600	Weak transcription	Esophagus	oesophagus
14	chr12:39688400-39726400	Weak transcription	Aorta	Aorta
15	chr12:39688800-39696800	Weak transcription	Brain Anterior Caudate	brain
16	chr12:39688800-39697200	Weak transcription	Left Ventricle	heart
17	chr12:39688800-39698200	Weak transcription	Brain Substantia Nigra	brain
18	chr12:39689000-39697800	Weak transcription	Brain Angular Gyrus	brain
19	chr12:39689000-39698400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:39689000-39699600	Weak transcription	Fetal Heart	heart
21	chr12:39689000-39724000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:39689400-39696400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:39689600-39696400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:39689600-39699000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:39689600-39702200	Weak transcription	Right Ventricle	heart
26	chr12:39689600-39725400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr12:39690400-39696200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:39690400-39703000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:39690400-39715200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:39690600-39701400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:39690600-39711600	Weak transcription	Placenta	Placenta
32	chr12:39690800-39697800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:39690800-39700800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:39690800-39704400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr12:39691800-39703400	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr12:39692200-39696800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:39692200-39697200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:39692400-39697800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:39692600-39697000	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:39693800-39705600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr12:39694000-39697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:39694000-39699800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr12:39694400-39696600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr12:39694600-39696600	Enhancers	Fetal Brain Male	brain
45	chr12:39694600-39697800	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr12:39694800-39697400	Enhancers	Fetal Lung	lung
47	chr12:39694800-39697600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr12:39694800-39699800	Weak transcription	HSMM	muscle
49	chr12:39695000-39696400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr12:39695000-39726400	Weak transcription	Fetal Intestine Large	intestine

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