Variant report

Variant	rs7970425
Chromosome Location	chr12:32452879-32452880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:32445285..32448075-chr12:32450808..32453523,2	MCF-7	breast:
2	chr12:32260676..32263344-chr12:32452464..32455287,2	MCF-7	breast:
3	chr12:32447000..32449614-chr12:32452651..32455475,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10771932	0.90[AFR][1000 genomes]
rs10771933	0.90[AFR][1000 genomes]
rs10771934	0.87[AFR][1000 genomes]
rs10844170	0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10844171	0.90[AFR][1000 genomes]
rs10844172	0.88[YRI][hapmap]
rs10844173	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs10844174	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs10844175	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs10844176	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs10844177	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs11051914	0.90[AFR][1000 genomes]
rs11051915	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs11051916	0.81[AFR][1000 genomes]
rs11051917	0.81[AFR][1000 genomes]
rs11051918	0.87[AFR][1000 genomes]
rs11051919	0.87[AFR][1000 genomes]
rs11051920	0.85[YRI][hapmap];0.87[AFR][1000 genomes]
rs11051921	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs12228804	0.87[AFR][1000 genomes]
rs12300478	0.87[AFR][1000 genomes]
rs12317439	0.83[AFR][1000 genomes]
rs12321268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28514337	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs325433	1.00[CEU][hapmap]
rs325435	0.87[CEU][hapmap]
rs34447944	0.81[EUR][1000 genomes]
rs4385975	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs55686847	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56144247	0.82[EUR][1000 genomes]
rs56235810	1.00[EUR][1000 genomes]
rs56880250	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73295804	0.83[EUR][1000 genomes]
rs73295807	0.83[EUR][1000 genomes]
rs73295812	0.83[EUR][1000 genomes]
rs73295822	0.83[EUR][1000 genomes]
rs7970001	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970657	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9988933	0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][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	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh 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	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv832366	chr12:32328559-32511360	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv2760249	chr12:32449115-32455620	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32427000-32458600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:32427000-32459400	Weak transcription	Aorta	Aorta
3	chr12:32427000-32463000	Weak transcription	NHLF	lung
4	chr12:32427200-32463000	Weak transcription	Fetal Intestine Small	intestine
5	chr12:32427600-32454400	Weak transcription	Primary B cells from cord blood	blood
6	chr12:32440200-32458600	Weak transcription	Thymus	Thymus
7	chr12:32443400-32461000	Weak transcription	Primary T cells from cord blood	blood
8	chr12:32443600-32454000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:32443600-32458600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr12:32443600-32458600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:32443600-32458600	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:32443600-32458600	Weak transcription	NH-A	brain
13	chr12:32443600-32458800	Weak transcription	HMEC	breast
14	chr12:32443600-32461200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr12:32443600-32463200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:32443600-32465000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr12:32443800-32458400	Weak transcription	HSMM	muscle
18	chr12:32443800-32458600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:32443800-32458600	Weak transcription	Ovary	ovary
20	chr12:32443800-32460200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:32443800-32464600	Weak transcription	NHDF-Ad	bronchial
22	chr12:32443800-32464800	Weak transcription	Brain Substantia Nigra	brain
23	chr12:32443800-32480400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:32444000-32460600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:32444200-32465000	Weak transcription	Hela-S3	cervix
26	chr12:32445200-32456000	Weak transcription	Dnd41	blood
27	chr12:32445200-32458800	Weak transcription	Fetal Stomach	stomach
28	chr12:32445400-32464000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:32445600-32458600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:32445600-32463600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:32445800-32464800	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:32446000-32461600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:32447000-32463000	Weak transcription	Brain Germinal Matrix	brain
34	chr12:32447400-32463000	Weak transcription	Fetal Thymus	thymus
35	chr12:32447600-32465000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:32447800-32458600	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:32448200-32463000	Weak transcription	HUVEC	blood vessel
38	chr12:32448400-32458600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr12:32448400-32463200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:32448600-32458800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:32448600-32461000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr12:32448600-32462600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr12:32449000-32458600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:32449000-32463000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr12:32449200-32458600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:32449200-32458600	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:32449200-32458600	Weak transcription	Osteobl	bone
48	chr12:32449200-32480400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:32449600-32490200	Weak transcription	HSMMtube	muscle
50	chr12:32449800-32453800	Weak transcription	GM12878-XiMat	blood

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