Variant report

Variant	rs7202234
Chromosome Location	chr16:11942322-11942323
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:11942094-11943032	K562	blood:	n/a	n/a
2	HEY1	chr16:11942285-11942648	K562	blood:	n/a	n/a
3	POLR2A	chr16:11942199-11943209	HepG2	liver:	n/a	n/a
4	POLR2A	chr16:11942257-11942571	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr16:11942306-11942768	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr16:11942129-11942450	MCF10A-Er-Src	breast:	n/a	n/a
7	RCOR1	chr16:11942079-11943552	IMR90	lung:	n/a	n/a
8	POLR2A	chr16:11942167-11942507	HepG2	liver:	n/a	n/a
9	POLR2A	chr16:11942006-11942666	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:11941930-11943150	GM12878	blood:	n/a	n/a
11	POLR2A	chr16:11942307-11942600	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr16:11942276-11943225	K562	blood:	n/a	n/a
13	POLR2A	chr16:11942297-11943384	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:11942266-11943376	GM12878	blood:	n/a	n/a
15	POLR2A	chr16:11941956-11943473	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:11941713..11946689-chr16:12006948..12011249,6	MCF-7	breast:
2	chr16:11889713..11895021-chr16:11941964..11945200,5	K562	blood:
3	chr16:11940299..11942446-chr16:11943353..11945680,3	K562	blood:
4	chr16:11942158..11945019-chr16:12007276..12009748,2	K562	blood:
5	chr16:11936442..11940721-chr16:11941344..11946764,13	K562	blood:
6	chr16:11834805..11837629-chr16:11940990..11944217,4	MCF-7	breast:

No data

Variant related genes	Relation type
RSL1D1	TF binding region
ENSG00000263307	TF binding region
ENSG00000171490	Chromatin interaction
ENSG00000153066	Chromatin interaction
ENSG00000266163	Chromatin interaction
ENSG00000103342	Chromatin interaction
ENSG00000262420	Chromatin interaction
ENSG00000263307	Chromatin interaction
ENSG00000122299	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1019814	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs10744977	0.93[ASN][1000 genomes]
rs11075022	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11646545	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11647818	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11649405	0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12925740	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs153025	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs154148	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs171656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2018199	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs2075158	0.88[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes]
rs2075159	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2098722	0.81[EUR][1000 genomes]
rs251723	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28279	0.84[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs33619	0.92[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap]
rs33623	0.92[CEU][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs33631	0.92[CEU][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs33635	0.88[CEU][hapmap]
rs33637	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs33640	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs33643	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33645	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs33647	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs33649	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs33651	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs33652	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs33653	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33655	0.92[CEU][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs33660	0.92[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35153773	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3971913	0.83[EUR][1000 genomes]
rs40311	0.92[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4511557	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs456325	0.88[CEU][hapmap]
rs718081	0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7185589	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7193470	0.87[ASN][1000 genomes]
rs7196913	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7197111	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7198817	0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8046617	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8047726	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8052900	0.83[EUR][1000 genomes]
rs8061189	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482288	chr16:11776491-11946429	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	nsv1043909	chr16:11839910-12007435	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7202234	TNFRSF17	cis	parietal	SCAN
rs7202234	RSL1D1	cis	parietal	SCAN
rs7202234	SOCS1	cis	parietal	SCAN
rs7202234	TNFRSF17	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:11918600-11943800	Weak transcription	Right Atrium	heart
2	chr16:11929200-11943000	Strong transcription	Lung	lung
3	chr16:11929200-11944000	Strong transcription	Fetal Stomach	stomach
4	chr16:11929400-11942800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr16:11929400-11942800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:11929400-11943000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr16:11929400-11943000	Strong transcription	Fetal Intestine Small	intestine
8	chr16:11929400-11943200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr16:11929400-11943400	Strong transcription	Brain Germinal Matrix	brain
10	chr16:11929400-11943600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr16:11929400-11943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr16:11929600-11942600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr16:11929600-11942600	Strong transcription	Thymus	Thymus
14	chr16:11929600-11943000	Strong transcription	Rectal Smooth Muscle	rectum
15	chr16:11929600-11943200	Strong transcription	Brain Anterior Caudate	brain
16	chr16:11929600-11943200	Strong transcription	Fetal Brain Female	brain
17	chr16:11929600-11943200	Strong transcription	Placenta Amnion	Placenta Amnion
18	chr16:11929600-11944000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr16:11929800-11942400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr16:11929800-11943200	Strong transcription	Primary hematopoietic stem cells	blood
21	chr16:11929800-11943400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr16:11929800-11943400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr16:11930000-11942400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr16:11930000-11942400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr16:11930000-11942600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr16:11930000-11942800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:11930000-11942800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr16:11930000-11943000	Strong transcription	Brain Cingulate Gyrus	brain
29	chr16:11930000-11943000	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr16:11930000-11943200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr16:11930000-11943200	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr16:11930000-11943400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr16:11930000-11943400	Strong transcription	Brain Angular Gyrus	brain
34	chr16:11930000-11943400	Strong transcription	Fetal Intestine Large	intestine
35	chr16:11930000-11943600	Strong transcription	Fetal Muscle Leg	muscle
36	chr16:11930000-11943800	Strong transcription	Liver	Liver
37	chr16:11930000-11944000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr16:11930000-11944000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr16:11930200-11943000	Strong transcription	Colon Smooth Muscle	Colon
40	chr16:11930200-11943200	Strong transcription	H9 Cell Line	embryonic stem cell
41	chr16:11930200-11943200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr16:11930200-11943200	Strong transcription	Colonic Mucosa	Colon
43	chr16:11930200-11943400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr16:11930200-11943400	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr16:11930200-11943400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr16:11930200-11943600	Strong transcription	Fetal Lung	lung
47	chr16:11930200-11943600	Strong transcription	Placenta	Placenta
48	chr16:11930200-11943800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr16:11930200-11943800	Strong transcription	Fetal Thymus	thymus
50	chr16:11930400-11943200	Strong transcription	iPS-15b Cell Line	embryonic stem cell

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