Variant report

Variant	rs4749
Chromosome Location	chr14:70793004-70793005
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70791685..70793470-chr14:70793914..70795967,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNJ2BP-1	chr14:70792785-70793166	NONHSAT037557

Variant related genes	Relation type
ENSG00000133983	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10130596	0.92[ASN][1000 genomes]
rs10132815	0.90[ASN][1000 genomes]
rs10134376	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10137455	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10139233	0.89[ASN][1000 genomes]
rs10140161	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10140263	0.89[ASN][1000 genomes]
rs10140916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10140938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10141034	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10142875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10146506	0.89[ASN][1000 genomes]
rs10146573	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10146684	0.89[ASN][1000 genomes]
rs10148810	0.89[ASN][1000 genomes]
rs10149724	0.84[ASN][1000 genomes]
rs10150618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10873232	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs11158851	0.86[EUR][1000 genomes]
rs11158856	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11620731	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11627279	0.80[ASN][1000 genomes]
rs12164868	0.85[ASN][1000 genomes]
rs12431557	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12433437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12434413	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[YRI][hapmap];0.95[ASN][1000 genomes]
rs12588332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12886764	0.92[ASN][1000 genomes]
rs12889915	0.92[ASN][1000 genomes]
rs17475866	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17476211	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2275297	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2275298	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2332278	0.86[CHB][hapmap]
rs2332279	0.86[CHB][hapmap]
rs2332363	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2332364	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2332366	0.82[ASN][1000 genomes]
rs2332368	0.89[ASN][1000 genomes]
rs2332369	0.89[ASN][1000 genomes]
rs2332370	0.89[ASN][1000 genomes]
rs2332371	0.89[ASN][1000 genomes]
rs2332374	0.89[ASN][1000 genomes]
rs2332375	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2332416	0.95[ASN][1000 genomes]
rs2332418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2332419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2332420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2332422	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2877656	0.92[ASN][1000 genomes]
rs2877658	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2877659	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2877660	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2877670	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3784155	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs4600398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4899344	0.92[ASN][1000 genomes]
rs4899345	0.89[ASN][1000 genomes]
rs4902814	0.90[ASN][1000 genomes]
rs6420899	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573948	0.92[ASN][1000 genomes]
rs6573950	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573951	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573953	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6573954	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573956	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573957	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6573958	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6573959	0.87[ASN][1000 genomes]
rs6573960	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7144850	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7145450	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7146414	0.89[ASN][1000 genomes]
rs7146493	0.89[ASN][1000 genomes]
rs7146553	0.89[ASN][1000 genomes]
rs7147906	0.89[ASN][1000 genomes]
rs7148114	0.89[ASN][1000 genomes]
rs7148889	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7150558	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7152300	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7152584	0.89[ASN][1000 genomes]
rs7154657	0.92[ASN][1000 genomes]
rs7155162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7155332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7155564	0.92[ASN][1000 genomes]
rs7155763	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7155967	0.92[ASN][1000 genomes]
rs7157399	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7157430	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7158117	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7158315	0.89[ASN][1000 genomes]
rs7159039	0.89[ASN][1000 genomes]
rs7159747	0.89[ASN][1000 genomes]
rs7160880	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8005386	0.85[ASN][1000 genomes]
rs8006423	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs8009793	0.87[ASN][1000 genomes]
rs8011014	0.89[ASN][1000 genomes]
rs8011156	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8013862	0.92[ASN][1000 genomes]
rs8017274	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs8021610	0.89[ASN][1000 genomes]
rs8022128	0.92[ASN][1000 genomes]
rs8022288	0.92[ASN][1000 genomes]
rs8022315	0.89[ASN][1000 genomes]
rs9323535	0.92[ASN][1000 genomes]
rs9323537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9788426	0.89[ASN][1000 genomes]
rs9788537	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902075	chr14:70612618-70919016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4749	VTI1B	cis	cerebellum	SCAN
rs4749	TTC9	cis	parietal	SCAN
rs4749	COX16	cis	cerebellum	SCAN
rs4749	COX16	cis	parietal	SCAN
rs4749	COX16	cis	multi-tissue	Pritchard

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70781200-70796800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr14:70783400-70799200	Weak transcription	NHEK	skin
3	chr14:70783600-70798600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr14:70784000-70801000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr14:70784200-70800600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr14:70784600-70798600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr14:70784800-70798800	Weak transcription	Gastric	stomach
8	chr14:70785400-70799200	Weak transcription	Stomach Mucosa	stomach
9	chr14:70785600-70799000	Weak transcription	Psoas Muscle	Psoas
10	chr14:70786000-70794400	Weak transcription	Fetal Intestine Large	intestine
11	chr14:70786000-70794600	Weak transcription	Fetal Intestine Small	intestine
12	chr14:70786000-70799200	Weak transcription	Pancreas	Pancrea
13	chr14:70788200-70813600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr14:70788600-70794400	Weak transcription	Left Ventricle	heart
15	chr14:70789000-70793600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr14:70789000-70798600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr14:70789200-70798600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:70789400-70798600	Weak transcription	Fetal Brain Female	brain
19	chr14:70789400-70798600	Weak transcription	Fetal Stomach	stomach
20	chr14:70789400-70798600	Weak transcription	Spleen	Spleen
21	chr14:70789400-70798800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr14:70789400-70799000	Weak transcription	Right Ventricle	heart
23	chr14:70789800-70798800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr14:70790000-70797600	Weak transcription	NHDF-Ad	bronchial
25	chr14:70790000-70798600	Weak transcription	Thymus	Thymus
26	chr14:70790200-70798600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr14:70790400-70793400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr14:70790400-70794400	Weak transcription	Aorta	Aorta
29	chr14:70790400-70794400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr14:70790400-70795600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr14:70790400-70796600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr14:70790400-70799000	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr14:70790400-70799200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr14:70790600-70796000	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr14:70790600-70798600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:70790600-70798800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr14:70790600-70799400	Weak transcription	Brain Anterior Caudate	brain
38	chr14:70790800-70794400	Weak transcription	Fetal Kidney	kidney
39	chr14:70790800-70795400	Strong transcription	Brain Germinal Matrix	brain
40	chr14:70790800-70795600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr14:70790800-70795600	Strong transcription	Liver	Liver
42	chr14:70790800-70796000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr14:70790800-70796200	Strong transcription	HSMM	muscle
44	chr14:70790800-70798600	Weak transcription	Esophagus	oesophagus
45	chr14:70791000-70795200	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr14:70791000-70795400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr14:70791000-70795600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr14:70791000-70795600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr14:70791000-70795800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr14:70791000-70796200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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