Variant report

Variant	rs4902448
Chromosome Location	chr14:39637849-39637850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:39624043..39626785-chr14:39637503..39639794,2	K562	blood:
2	chr14:39637610..39639234-chr14:39680366..39682544,2	MCF-7	breast:
3	chr14:39636723..39639312-chr14:39766672..39768267,2	MCF-7	breast:
4	chr14:39631838..39633415-chr14:39636342..39639514,3	MCF-7	breast:
5	chr14:39635717..39639064-chr14:39734944..39738287,4	MCF-7	breast:
6	chr14:39602771..39604896-chr14:39637781..39640211,2	MCF-7	breast:
7	chr14:39636108..39642775-chr14:39734196..39739360,12	MCF-7	breast:
8	chr14:39570654..39572608-chr14:39637696..39639686,2	K562	blood:
9	chr14:39570348..39574070-chr14:39637691..39640941,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258671	Chromatin interaction
ENSG00000258940	Chromatin interaction
ENSG00000150527	Chromatin interaction
ENSG00000100934	Chromatin interaction
ENSG00000258651	Chromatin interaction
ENSG00000241984	Chromatin interaction
ENSG00000258941	Chromatin interaction
ENSG00000092208	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10130972	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10133797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10136536	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10149120	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10151683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs11157041	0.86[CHB][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap]
rs12147991	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12437405	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12885242	0.86[CHB][hapmap];0.87[GIH][hapmap]
rs12891258	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12894046	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12895751	0.81[EUR][1000 genomes]
rs13379360	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17108846	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2737721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2737729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28379470	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28485301	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2869	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28856917	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34816815	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35035794	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3742354	0.93[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap]
rs3759545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4143954	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902405	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902406	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902418	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902431	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902435	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs532	0.81[CEU][hapmap];0.83[EUR][1000 genomes]
rs58851254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62640373	0.84[AFR][1000 genomes]
rs67248626	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71407780	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7147194	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153124	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73291567	0.84[AFR][1000 genomes]
rs73291573	0.84[AFR][1000 genomes]
rs73291583	0.84[AFR][1000 genomes]
rs73291585	0.84[AFR][1000 genomes]
rs73291588	0.84[AFR][1000 genomes]
rs8006879	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009933	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs9322992	0.86[CHB][hapmap]
rs9322994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1051247	chr14:39604035-39652789	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv1813567	chr14:39632114-39642840	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4902448	SIP1	Cis_1M	lymphoblastoid	RTeQTL
rs4902448	SSTR1	cis	parietal	SCAN
rs4902448	TRAPPC6B	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39584200-39638600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:39611200-39638800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:39611400-39638000	Weak transcription	A549	lung
4	chr14:39621000-39638400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr14:39624400-39638000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr14:39627000-39638800	Weak transcription	Gastric	stomach
7	chr14:39627200-39638600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr14:39631600-39638600	Weak transcription	Esophagus	oesophagus
9	chr14:39631800-39638600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr14:39632200-39638000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr14:39632200-39638600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr14:39632200-39638600	Weak transcription	Pancreas	Pancrea
13	chr14:39632400-39638600	Weak transcription	Lung	lung
14	chr14:39633000-39638000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr14:39633400-39638200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr14:39634200-39638000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:39634200-39638600	Weak transcription	Left Ventricle	heart
18	chr14:39634200-39638800	Weak transcription	Spleen	Spleen
19	chr14:39635000-39638000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr14:39635000-39638000	Weak transcription	Right Ventricle	heart
21	chr14:39635000-39638800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr14:39635200-39638200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr14:39635400-39638000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr14:39635400-39638800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr14:39635600-39638800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr14:39636000-39638600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr14:39636000-39638600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr14:39636000-39638600	Weak transcription	Placenta	Placenta
29	chr14:39636200-39638000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr14:39636200-39638800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr14:39636200-39640200	Active TSS	GM12878-XiMat	blood
32	chr14:39636400-39638400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr14:39636400-39638600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr14:39636600-39638000	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr14:39636800-39638200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr14:39636800-39640600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr14:39637000-39638000	Enhancers	Primary T cells from cord blood	blood
38	chr14:39637000-39638000	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr14:39637000-39638000	Enhancers	Fetal Intestine Large	intestine
40	chr14:39637000-39638400	Enhancers	Small Intestine	intestine
41	chr14:39637000-39638800	Weak transcription	Stomach Mucosa	stomach
42	chr14:39637200-39638200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr14:39637200-39638600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
44	chr14:39637400-39638000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr14:39637400-39638000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr14:39637400-39638000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr14:39637400-39638000	Enhancers	Brain Hippocampus Middle	brain
48	chr14:39637400-39638000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr14:39637400-39638200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr14:39637400-39638200	Enhancers	Rectal Smooth Muscle	rectum

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