Variant report

Variant	rs2303788
Chromosome Location	chr16:71497918-71497919
allele	A/C
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:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71490751..71498047-chr16:71514421..71521729,20	MCF-7	breast:
2	chr16:71492243..71500079-chr16:71512817..71521299,31	MCF-7	breast:
3	chr16:71497700..71500390-chr16:71504714..71506907,2	K562	blood:
4	chr16:71492651..71498511-chr16:71515020..71523604,17	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CHST4-3	chr16:71497161-71499844	ENSG00000247324
2	lnc-CHST4-3	chr16:71497836-71497970	ENSG00000247324.2

No data

Variant related genes	Relation type
ENSG00000261611	Chromatin interaction
ENSG00000157429	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10500558	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11640165	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11641492	0.93[ASN][1000 genomes]
rs11643216	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11644434	0.95[CEU][hapmap];0.82[CHB][hapmap];0.80[EUR][1000 genomes]
rs11645711	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11647749	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12446461	0.88[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs13331346	0.93[ASN][1000 genomes]
rs1609868	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1609869	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16973266	0.80[CHB][hapmap];0.81[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes]
rs2004672	0.91[ASN][1000 genomes]
rs2070832	0.88[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs2288486	0.82[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs2288487	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288488	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28372238	0.91[ASN][1000 genomes]
rs310334	0.97[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs35373081	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35916432	0.90[ASN][1000 genomes]
rs36063092	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3813743	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs4149498	0.89[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4503795	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4620964	0.82[ASN][1000 genomes]
rs58134724	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58452291	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58719913	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6499523	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7184543	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7186241	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7187165	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7187354	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7188342	0.94[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs7199026	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs7199373	0.93[ASN][1000 genomes]
rs7200335	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7200431	0.85[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7202662	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7202953	0.92[ASN][1000 genomes]
rs730470	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs732318	0.88[CHB][hapmap];0.95[CHD][hapmap];0.80[JPT][hapmap];0.86[ASN][1000 genomes]
rs74026831	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74027246	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8044068	0.91[ASN][1000 genomes]
rs8044561	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs8051212	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs8053662	0.92[ASN][1000 genomes]
rs8058294	0.87[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs8058776	0.86[ASN][1000 genomes]
rs8061078	0.82[CHB][hapmap]
rs9302623	0.98[ASN][1000 genomes]
rs9926110	0.88[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs9928243	0.88[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9933680	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9935426	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs9936249	0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs9940771	0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[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	nsv949461	chr16:71196153-71579711	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2303788	SLC9A5	cis	cerebellum	SCAN
rs2303788	COG8	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71496400-71509400	Weak transcription	Small Intestine	intestine
2	chr16:71496600-71507600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr16:71496600-71508400	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr16:71496600-71508400	Weak transcription	Placenta	Placenta
5	chr16:71496600-71509200	Weak transcription	Fetal Intestine Large	intestine
6	chr16:71496600-71509400	Weak transcription	Colonic Mucosa	Colon
7	chr16:71496600-71509400	Weak transcription	Esophagus	oesophagus
8	chr16:71496600-71509400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr16:71496600-71511400	Weak transcription	Pancreas	Pancrea
10	chr16:71496800-71498200	Weak transcription	K562	blood
11	chr16:71496800-71505000	Weak transcription	Liver	Liver
12	chr16:71496800-71507600	Weak transcription	Ovary	ovary
13	chr16:71496800-71507800	Weak transcription	Fetal Muscle Leg	muscle
14	chr16:71496800-71507800	Weak transcription	Left Ventricle	heart
15	chr16:71496800-71507800	Weak transcription	HSMM	muscle
16	chr16:71496800-71507800	Weak transcription	HSMMtube	muscle
17	chr16:71496800-71508400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr16:71496800-71508600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr16:71496800-71508600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr16:71496800-71508600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr16:71496800-71508800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr16:71496800-71508800	Weak transcription	Primary T cells from cord blood	blood
23	chr16:71496800-71508800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr16:71496800-71508800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr16:71496800-71508800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr16:71496800-71509000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr16:71496800-71509200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr16:71496800-71509400	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr16:71496800-71509400	Weak transcription	Psoas Muscle	Psoas
30	chr16:71496800-71512000	Weak transcription	Rectal Smooth Muscle	rectum
31	chr16:71496800-71512200	Weak transcription	Fetal Intestine Small	intestine
32	chr16:71497000-71498000	Enhancers	Brain Germinal Matrix	brain
33	chr16:71497000-71503600	Weak transcription	Adipose Nuclei	Adipose
34	chr16:71497000-71504200	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:71497000-71504400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr16:71497000-71504400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr16:71497000-71504600	Weak transcription	Stomach Smooth Muscle	stomach
38	chr16:71497000-71507800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr16:71497000-71507800	Weak transcription	NHLF	lung
40	chr16:71497000-71508000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr16:71497000-71508400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr16:71497000-71508600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr16:71497000-71511800	Weak transcription	Brain Substantia Nigra	brain
44	chr16:71497000-71517400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr16:71497000-71517400	Weak transcription	Fetal Heart	heart
46	chr16:71497000-71517600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr16:71497200-71504600	Weak transcription	Fetal Brain Female	brain
48	chr16:71497200-71504800	Weak transcription	Aorta	Aorta
49	chr16:71497200-71504800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr16:71497200-71504800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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