Variant report

Variant	rs9940234
Chromosome Location	chr16:71964805-71964806
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:71958112..71959860-chr16:71963108..71964855,2	K562	blood:
2	chr16:71927384..71929645-chr16:71963039..71965792,3	MCF-7	breast:
3	chr16:71927209..71930992-chr16:71962077..71965220,3	K562	blood:
4	chr16:71955110..71958047-chr16:71963028..71965520,2	MCF-7	breast:
5	chr16:71927209..71930992-chr16:71962077..71965660,4	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IST1-1	chr16:71963914-71965102	ENSG00000263320.1

No data

Variant related genes	Relation type
ENSG00000182149	Chromatin interaction
ENSG00000102984	Chromatin interaction
ENSG00000261337	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10500567	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10852505	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap]
rs10852507	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11075906	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11075909	0.87[YRI][hapmap]
rs11075910	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11639843	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11640135	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11642529	1.00[CHB][hapmap]
rs11644740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11648557	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11861296	0.82[GIH][hapmap];0.82[JPT][hapmap]
rs11865456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149460	0.82[JPT][hapmap]
rs12149917	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12445564	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445641	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12448086	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12708919	1.00[CHB][hapmap]
rs12921279	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12921459	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12927691	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12928939	0.82[GIH][hapmap]
rs12934512	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13330178	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17357420	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17358402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288030	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2878494	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3088285	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34029919	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34101687	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34664834	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35028754	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35069141	0.81[ASN][1000 genomes]
rs35209006	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35377660	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35404791	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35535529	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35595148	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs36182990	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751820	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4528577	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4788568	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4788575	0.85[JPT][hapmap]
rs4788579	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs71384781	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71384782	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71386939	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs71386940	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71386942	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7185027	0.82[AFR][1000 genomes]
rs7187418	0.87[YRI][hapmap]
rs7188591	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7191848	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195988	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7197486	0.87[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7198834	0.87[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7202840	1.00[CHB][hapmap];0.82[GIH][hapmap]
rs73586164	0.86[ASN][1000 genomes]
rs8046044	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8049508	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8050058	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8051878	1.00[CHB][hapmap]
rs8052358	0.87[ASW][hapmap];0.95[CEU][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8053906	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8054602	0.87[YRI][hapmap]
rs8063657	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9939404	0.86[YRI][hapmap]
rs9939911	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9940234	ZFHX3	cis	parietal	SCAN
rs9940234	PHLPP2	cis	lymphoblastoid	seeQTL
rs9940234	TK2	cis	parietal	SCAN
rs9940234	TMEM208	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71948400-71965600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr16:71948800-71966000	Strong transcription	HUES64 Cell Line	embryonic stem cell
3	chr16:71948800-71966200	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr16:71948800-71968800	Strong transcription	Dnd41	blood
5	chr16:71948800-71969600	Strong transcription	Fetal Intestine Large	intestine
6	chr16:71949000-71966200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr16:71949200-71966600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr16:71949200-71969600	Strong transcription	Fetal Thymus	thymus
9	chr16:71949400-71965200	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr16:71949400-71965800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr16:71950600-71965400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr16:71950600-71969600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr16:71950800-71968800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr16:71953200-71965000	Strong transcription	Primary B cells from peripheral blood	blood
15	chr16:71953200-71965400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr16:71953200-71969600	Strong transcription	Liver	Liver
17	chr16:71953800-71965600	Strong transcription	Thymus	Thymus
18	chr16:71953800-71966800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr16:71953800-71969000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr16:71953800-71969600	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr16:71954000-71965200	Strong transcription	Primary B cells from cord blood	blood
22	chr16:71954000-71969000	Strong transcription	GM12878-XiMat	blood
23	chr16:71954000-71969000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr16:71954000-71969400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr16:71954000-71969600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr16:71954200-71968200	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr16:71954200-71969800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr16:71955000-71969000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr16:71956800-71971000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr16:71958000-71969400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr16:71960400-71965000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr16:71961000-71966000	Strong transcription	Primary T cells from cord blood	blood
33	chr16:71961200-71966400	Strong transcription	HepG2	liver
34	chr16:71961600-71965200	Weak transcription	Stomach Mucosa	stomach
35	chr16:71961600-71965400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr16:71961800-71965000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr16:71961800-71969600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr16:71962000-71965000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr16:71962000-71971200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr16:71962200-71965000	Strong transcription	Sigmoid Colon	Sigmoid Colon
41	chr16:71962400-71967800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr16:71962600-71967600	Weak transcription	Colonic Mucosa	Colon
43	chr16:71962600-71967800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr16:71962600-71967800	Weak transcription	Aorta	Aorta
45	chr16:71962600-71967800	Weak transcription	Pancreas	Pancrea
46	chr16:71962600-71969600	Strong transcription	Placenta	Placenta
47	chr16:71962600-71972000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr16:71963000-71967600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr16:71963200-71966200	Weak transcription	Spleen	Spleen
50	chr16:71963200-71966400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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