Variant report

Variant	rs7148185
Chromosome Location	chr14:24520604-24520605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:24520414-24520853	GM12892	blood:	n/a	n/a
2	MAX	chr14:24520517-24522635	HepG2	liver:	n/a	chr14:24521174-24521184 chr14:24521197-24521207
3	JUND	chr14:24520086-24520629	HepG2	liver:	n/a	n/a
4	MAZ	chr14:24520534-24522079	IMR90	lung:	n/a	chr14:24521174-24521184 chr14:24521197-24521207
5	POLR2A	chr14:24520466-24521412	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYBL2	chr14:24520368-24522162	HepG2	liver:	n/a	n/a
7	MAX	chr14:24520435-24522262	MCF-7	breast:	n/a	chr14:24521174-24521184 chr14:24521197-24521207
8	MXI1	chr14:24520375-24522558	SK-N-SH	brain:	n/a	n/a
9	POLR2A	chr14:24520430-24521809	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr14:24520497-24521246	GM12878	blood:	n/a	n/a
11	POLR2A	chr14:24520363-24520843	GM12892	blood:	n/a	n/a
12	REST	chr14:24520411-24522145	H1-neurons	neurons:	n/a	chr14:24521782-24521800 chr14:24521265-24521275 chr14:24521781-24521801 chr14:24521784-24521797 chr14:24521464-24521477 chr14:24521200-24521213 chr14:24521556-24521569 chr14:24521164-24521177 chr14:24521161-24521174 chr14:24521556-24521569 chr14:24521787-24521801 chr14:24521781-24521801 chr14:24521336-24521349 chr14:24521554-24521572 chr14:24521781-24521794
13	POLR2A	chr14:24520073-24521406	GM12892	blood:	n/a	n/a
14	POLR2A	chr14:24520603-24521307	GM19193	blood:	n/a	n/a
15	MTA3	chr14:24520566-24521203	GM12878	blood:	n/a	n/a
16	POLR2A	chr14:24520535-24521831	H1-neurons	neurons:	n/a	n/a
17	FOSL2	chr14:24520048-24520734	HepG2	liver:	n/a	n/a
18	POLR2A	chr14:24520569-24521338	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:24519494..24523801-chr14:24562244..24565641,8	MCF-7	breast:
2	chr14:24519207..24521902-chr14:24608488..24612189,3	MCF-7	breast:
3	chr14:24505124..24506975-chr14:24520204..24522367,2	MCF-7	breast:
4	chr14:24519507..24523114-chr14:24581353..24584961,4	MCF-7	breast:
5	chr14:24519379..24521106-chr14:24565277..24567591,2	MCF-7	breast:
6	chr14:24519595..24523490-chr14:24615649..24620329,4	MCF-7	breast:
7	chr14:24520169..24522570-chr14:24571507..24573400,2	MCF-7	breast:
8	chr14:24519308..24521603-chr14:24550146..24552325,2	K562	blood:
9	chr14:24519146..24523502-chr14:24549476..24554002,6	MCF-7	breast:

Variant related genes	Relation type
LRRC16B	TF binding region
ENSG00000092098	Chromatin interaction
ENSG00000225766	Chromatin interaction
ENSG00000100889	Chromatin interaction
ENSG00000100911	Chromatin interaction
ENSG00000129535	Chromatin interaction
ENSG00000259321	Chromatin interaction
ENSG00000100908	Chromatin interaction
ENSG00000100897	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11158525	0.85[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11626841	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2877590	0.81[EUR][1000 genomes]
rs62000819	0.83[EUR][1000 genomes]
rs6573541	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152726	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs8017358	0.85[GIH][hapmap]
rs9972282	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3405661	chr14:24189883-24670942	Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv1049316	chr14:24405420-24583724	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
3	nsv541999	chr14:24405420-24583724	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
4	nsv564047	chr14:24428509-24525634	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1052180	chr14:24429298-24555710	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv1037929	chr14:24478882-24522447	Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv1043854	chr14:24488131-24522447	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
8	nsv516023	chr14:24489605-24550224	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv983808	chr14:24503854-24523979	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
10	nsv1036658	chr14:24513905-24555710	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	esv1827678	chr14:24520544-24663325	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7148185	SAG	trans	parietal	SCAN
rs7148185	LRRC16B	cis	cerebellum	SCAN
rs7148185	YME1L1	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24519400-24520800	Weak transcription	Primary B cells from cord blood	blood
2	chr14:24520200-24521800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr14:24520200-24522200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr14:24520400-24520800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr14:24520400-24520800	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr14:24520400-24521000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
7	chr14:24520400-24521000	Flanking Active TSS	Fetal Brain Male	brain
8	chr14:24520400-24521400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr14:24520400-24521400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr14:24520400-24521400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr14:24520400-24521600	Active TSS	Brain Anterior Caudate	brain
12	chr14:24520400-24521600	Active TSS	Brain Hippocampus Middle	brain
13	chr14:24520400-24521800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr14:24520400-24521800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr14:24520400-24521800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr14:24520400-24521800	Active TSS	Brain Cingulate Gyrus	brain
17	chr14:24520400-24521800	Active TSS	Brain Substantia Nigra	brain
18	chr14:24520400-24521800	Enhancers	Fetal Heart	heart
19	chr14:24520400-24522000	Flanking Active TSS	GM12878-XiMat	blood
20	chr14:24520400-24522200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr14:24520400-24522200	Flanking Active TSS	Dnd41	blood
22	chr14:24520600-24520800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr14:24520600-24520800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:24520600-24520800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr14:24520600-24520800	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr14:24520600-24520800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr14:24520600-24520800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr14:24520600-24520800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
29	chr14:24520600-24520800	Enhancers	Primary hematopoietic stem cells	blood
30	chr14:24520600-24520800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
31	chr14:24520600-24520800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr14:24520600-24520800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr14:24520600-24520800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr14:24520600-24520800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:24520600-24520800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr14:24520600-24520800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr14:24520600-24520800	Active TSS	Liver	Liver
38	chr14:24520600-24520800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
39	chr14:24520600-24520800	Flanking Active TSS	Fetal Brain Female	brain
40	chr14:24520600-24520800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
41	chr14:24520600-24520800	Flanking Active TSS	Fetal Lung	lung
42	chr14:24520600-24520800	Enhancers	Placenta	Placenta
43	chr14:24520600-24520800	Enhancers	Left Ventricle	heart
44	chr14:24520600-24520800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr14:24520600-24520800	Enhancers	Psoas Muscle	Psoas
46	chr14:24520600-24520800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr14:24520600-24520800	Flanking Bivalent TSS/Enh	HMEC	breast
48	chr14:24520600-24520800	Bivalent Enhancer	NH-A	brain
49	chr14:24520600-24520800	Flanking Bivalent TSS/Enh	NHEK	skin
50	chr14:24520600-24521000	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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