Variant report

Variant	rs7138398
Chromosome Location	chr12:123341833-123341834
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr12:123341805-123342262	HepG2	liver:	n/a	n/a
2	JUND	chr12:123341829-123342132	HepG2	liver:	n/a	n/a
3	FOXA1	chr12:123341763-123342315	HepG2	liver:	n/a	n/a
4	GATA2	chr12:123341706-123342337	SH-SY5Y	brain:	n/a	n/a
5	GATA3	chr12:123341818-123342164	T-47D	breast:	n/a	n/a
6	POLR2A	chr12:123341429-123342046	PANC-1	pancreas:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:123341218..123343418-chr12:123435392..123437282,2	MCF-7	breast:
2	chr12:123341647..123346113-chr12:123465146..123467618,4	K562	blood:
3	chr12:123329734..123338030-chr12:123339120..123345153,11	MCF-7	breast:
4	chr12:123330610..123333935-chr12:123339820..123343037,3	MCF-7	breast:
5	chr11:65265725..65268508-chr12:123341267..123343973,2	MCF-7	breast:
6	chr12:123340470..123342158-chr12:123459989..123462897,2	K562	blood:
7	chr12:123319098..123320683-chr12:123341200..123343169,2	MCF-7	breast:

No data

Variant related genes	Relation type
HIP1R	TF binding region
ENSG00000111325	Chromatin interaction
ENSG00000182196	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000270117	Chromatin interaction
ENSG00000251562	Chromatin interaction
ENSG00000150967	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10744422	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10744434	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10773627	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10773657	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10847826	0.87[EUR][1000 genomes]
rs10847869	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11060064	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs11060065	0.86[CHB][hapmap];0.88[JPT][hapmap]
rs12255	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12298151	0.93[ASN][1000 genomes]
rs12298664	0.80[ASN][1000 genomes]
rs12299742	0.80[ASN][1000 genomes]
rs12313006	0.91[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs12314494	0.80[ASN][1000 genomes]
rs12314544	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs12319654	0.80[ASN][1000 genomes]
rs12369846	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12426809	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1532835	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1587856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1671685	0.80[ASN][1000 genomes]
rs1696320	0.81[CHB][hapmap]
rs1696326	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1696349	0.80[ASN][1000 genomes]
rs1799618	0.91[CHB][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1979236	0.80[ASN][1000 genomes]
rs1979237	0.80[ASN][1000 genomes]
rs2061098	1.00[EUR][1000 genomes]
rs2061101	0.92[EUR][1000 genomes]
rs2100500	0.80[ASN][1000 genomes]
rs2135014	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2271049	1.00[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2271050	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2271051	0.91[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs2292131	0.80[ASN][1000 genomes]
rs2292132	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2292134	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2292135	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2292136	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2292138	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292139	0.93[ASN][1000 genomes]
rs2343108	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2343109	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343685	0.87[EUR][1000 genomes]
rs2649909	0.80[ASN][1000 genomes]
rs2880678	0.87[EUR][1000 genomes]
rs3817094	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3825143	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3852536	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3852537	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4759355	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4759381	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759382	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759386	0.98[EUR][1000 genomes]
rs4759387	0.98[EUR][1000 genomes]
rs4759389	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs4759393	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs56272219	0.80[ASN][1000 genomes]
rs59192320	0.94[ASN][1000 genomes]
rs59922385	0.80[ASN][1000 genomes]
rs6489245	1.00[CEU][hapmap]
rs6489247	0.91[CEU][hapmap]
rs7139055	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7294991	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs7303024	0.80[ASN][1000 genomes]
rs7309225	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs73421642	0.80[ASN][1000 genomes]
rs735378	0.80[ASN][1000 genomes]
rs754080	0.80[ASN][1000 genomes]
rs7957643	0.80[CEU][hapmap]
rs7959441	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7972447	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7980541	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs839360	0.91[CHB][hapmap]
rs897385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs897391	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs897392	0.82[ASN][1000 genomes]
rs897393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs921808	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs936083	0.82[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs937520	0.80[ASN][1000 genomes]
rs937766	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv899576	chr12:123335527-123528405	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7138398	CCDC62	cis	Thyroid	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123322800-123353000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr12:123323200-123352000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr12:123324600-123344800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr12:123324600-123352800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:123324800-123351600	Weak transcription	Small Intestine	intestine
6	chr12:123326600-123345000	Weak transcription	A549	lung
7	chr12:123327200-123344200	Weak transcription	Hela-S3	cervix
8	chr12:123327400-123352600	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr12:123327600-123353400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:123329200-123355000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr12:123329600-123344600	Strong transcription	Fetal Intestine Small	intestine
12	chr12:123330400-123344400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr12:123330400-123349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:123332200-123343200	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:123332600-123344800	Strong transcription	Duodenum Mucosa	Duodenum
16	chr12:123332600-123355600	Strong transcription	Thymus	Thymus
17	chr12:123333000-123344400	Strong transcription	Spleen	Spleen
18	chr12:123333000-123344600	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr12:123333000-123345000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr12:123333800-123342800	Weak transcription	Ovary	ovary
21	chr12:123334400-123344400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:123335200-123347000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr12:123335600-123342600	Strong transcription	Primary T cells from cord blood	blood
24	chr12:123336000-123342400	Genic enhancers	Brain Inferior Temporal Lobe	brain
25	chr12:123337200-123343400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:123337200-123348800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr12:123337400-123348400	Weak transcription	HSMM	muscle
28	chr12:123337400-123356200	Weak transcription	Fetal Kidney	kidney
29	chr12:123337600-123344200	Weak transcription	Placenta	Placenta
30	chr12:123337600-123344800	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr12:123337600-123348200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:123337600-123351000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:123337600-123351400	Weak transcription	HSMMtube	muscle
34	chr12:123337800-123342600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr12:123337800-123344800	Strong transcription	NHEK	skin
36	chr12:123337800-123346800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:123337800-123347600	Weak transcription	NH-A	brain
38	chr12:123337800-123351600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:123338000-123342000	Genic enhancers	Brain Substantia Nigra	brain
40	chr12:123338200-123343000	Strong transcription	Liver	Liver
41	chr12:123338400-123342400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:123338400-123344600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:123338400-123344800	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr12:123338400-123344800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:123338400-123345200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr12:123338400-123350400	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:123338400-123351000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:123338600-123342000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:123338600-123342000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr12:123338600-123344400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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