Variant report

Variant	rs3896870
Chromosome Location	chr12:123333611-123333612
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123329734..123338030-chr12:123339120..123345153,11	MCF-7	breast:
2	chr12:123330610..123333935-chr12:123339820..123343037,3	MCF-7	breast:
3	chr12:123331248..123334066-chr12:123346925..123349387,2	K562	blood:
4	chr12:123329055..123330600-chr12:123330820..123333817,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130787	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10773627	0.84[ASN][1000 genomes]
rs10773657	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10847826	0.84[ASN][1000 genomes]
rs10847869	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12426809	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1532835	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2135014	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2271049	0.80[ASN][1000 genomes]
rs2292132	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2292134	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292135	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2343108	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2343685	0.84[ASN][1000 genomes]
rs2880678	0.84[ASN][1000 genomes]
rs3817094	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3852536	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4759355	0.80[ASN][1000 genomes]
rs4759389	0.84[ASN][1000 genomes]
rs897391	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs897392	0.86[ASN][1000 genomes]
rs897393	0.84[ASN][1000 genomes]
rs921808	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs937766	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3388790	chr12:123275902-123655103	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv899572	chr12:123292503-123477311	Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv899573	chr12:123312051-123528405	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
5	nsv517200	chr12:123312051-123654498	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv899574	chr12:123316566-123360151	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv560490	chr12:123326374-123346971	Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv899575	chr12:123326374-123360151	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3896870	CCDC62	cis	Thyroid	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123321800-123336800	Weak transcription	Aorta	Aorta
2	chr12:123322800-123334000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr12:123322800-123334400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:123322800-123339600	Weak transcription	Dnd41	blood
5	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr12:123323200-123340800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:123323400-123335200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:123323600-123340800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:123324600-123344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr12:123324800-123351600	Weak transcription	Small Intestine	intestine
13	chr12:123325000-123338400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:123325200-123335400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:123326600-123335600	Weak transcription	NHLF	lung
16	chr12:123326600-123336800	Weak transcription	Psoas Muscle	Psoas
17	chr12:123326600-123345000	Weak transcription	A549	lung
18	chr12:123326800-123335400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:123327200-123337000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:123327200-123340000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr12:123327200-123344200	Weak transcription	Hela-S3	cervix
22	chr12:123327400-123336400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:123327400-123352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:123327600-123334200	Weak transcription	Adipose Nuclei	Adipose
25	chr12:123327600-123335400	Weak transcription	HUVEC	blood vessel
26	chr12:123327600-123337000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:123327600-123353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr12:123328200-123336800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:123328400-123336200	Weak transcription	Placenta	Placenta
30	chr12:123329200-123335600	Weak transcription	Primary T cells from cord blood	blood
31	chr12:123329200-123337600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr12:123329200-123355000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:123329400-123341800	Weak transcription	HepG2	liver
34	chr12:123329600-123336600	Strong transcription	Fetal Stomach	stomach
35	chr12:123329600-123344600	Strong transcription	Fetal Intestine Small	intestine
36	chr12:123330000-123335400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr12:123330000-123340400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr12:123330400-123335400	Weak transcription	Right Atrium	heart
39	chr12:123330400-123344400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr12:123330400-123349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:123330800-123334200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr12:123330800-123335400	Weak transcription	Fetal Brain Male	brain
43	chr12:123330800-123335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:123330800-123336800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr12:123331000-123333800	Weak transcription	Fetal Heart	heart
46	chr12:123331000-123335400	Weak transcription	Stomach Mucosa	stomach
47	chr12:123331000-123335400	Weak transcription	HMEC	breast
48	chr12:123331000-123337000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:123331000-123340800	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:123331200-123336800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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