Variant report

Variant	rs2103144
Chromosome Location	chr7:17940152-17940153
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:17940123-17940285	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
SNX13	TF binding region

Extended variants
information (count: 167 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs10216315	0.87[ASN][1000 genomes]
rs10227224	0.86[ASN][1000 genomes]
rs10227501	0.82[ASN][1000 genomes]
rs10227582	0.86[ASN][1000 genomes]
rs10231926	0.82[ASN][1000 genomes]
rs10264355	0.89[EUR][1000 genomes]
rs10264445	0.83[EUR][1000 genomes]
rs10264447	0.81[EUR][1000 genomes]
rs10265373	0.88[ASN][1000 genomes]
rs1051603	0.91[EUR][1000 genomes]
rs11768866	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11983260	0.87[ASN][1000 genomes]
rs12699918	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1357796	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1404414	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1404421	0.88[EUR][1000 genomes]
rs1404422	0.89[EUR][1000 genomes]
rs1404424	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1404425	0.89[EUR][1000 genomes]
rs1524774	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1524775	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1524777	0.89[EUR][1000 genomes]
rs1568815	0.90[ASN][1000 genomes]
rs1568817	0.89[ASN][1000 genomes]
rs1568818	0.89[ASN][1000 genomes]
rs1830006	0.89[EUR][1000 genomes]
rs1852010	0.89[EUR][1000 genomes]
rs1852011	0.87[EUR][1000 genomes]
rs1965534	0.89[EUR][1000 genomes]
rs1997019	0.89[EUR][1000 genomes]
rs2030725	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2140710	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2177652	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2254176	0.89[EUR][1000 genomes]
rs2462512	0.90[EUR][1000 genomes]
rs2691552	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2691553	0.89[EUR][1000 genomes]
rs2691555	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2691557	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691558	0.89[ASN][1000 genomes]
rs2691559	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2691560	0.90[ASN][1000 genomes]
rs2691561	0.90[ASN][1000 genomes]
rs2691562	0.90[ASN][1000 genomes]
rs2691563	0.90[ASN][1000 genomes]
rs2691564	0.90[ASN][1000 genomes]
rs2691566	0.90[ASN][1000 genomes]
rs2691567	0.89[ASN][1000 genomes]
rs2691568	0.90[ASN][1000 genomes]
rs2691569	0.90[ASN][1000 genomes]
rs2691570	0.90[ASN][1000 genomes]
rs2691571	0.90[ASN][1000 genomes]
rs2691577	0.86[ASN][1000 genomes]
rs2691578	0.86[ASN][1000 genomes]
rs2691579	0.84[ASN][1000 genomes]
rs2691580	0.85[ASN][1000 genomes]
rs2691581	0.89[EUR][1000 genomes]
rs2691582	0.89[EUR][1000 genomes]
rs2691583	0.88[EUR][1000 genomes]
rs2691585	0.89[EUR][1000 genomes]
rs2691586	0.89[EUR][1000 genomes]
rs2691589	0.88[EUR][1000 genomes]
rs2691592	0.88[EUR][1000 genomes]
rs2691593	0.88[EUR][1000 genomes]
rs2691594	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2691595	0.88[EUR][1000 genomes]
rs2691596	0.88[EUR][1000 genomes]
rs2691597	0.92[EUR][1000 genomes]
rs2691600	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2691601	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2691602	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2691604	0.89[EUR][1000 genomes]
rs2691605	0.94[EUR][1000 genomes]
rs2691607	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691609	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2691610	0.89[EUR][1000 genomes]
rs2691611	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2691612	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2691613	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2691615	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2691616	0.89[EUR][1000 genomes]
rs2691617	0.82[EUR][1000 genomes]
rs2691618	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2691620	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2691621	0.89[EUR][1000 genomes]
rs2691623	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2691625	0.87[EUR][1000 genomes]
rs2691627	0.89[EUR][1000 genomes]
rs2691628	0.89[EUR][1000 genomes]
rs2691629	0.89[EUR][1000 genomes]
rs2691630	0.89[EUR][1000 genomes]
rs2714855	0.86[ASN][1000 genomes]
rs2714857	0.87[ASN][1000 genomes]
rs2714859	0.89[ASN][1000 genomes]
rs2714860	0.90[ASN][1000 genomes]
rs2714861	0.90[ASN][1000 genomes]
rs2714863	0.89[ASN][1000 genomes]
rs2714864	0.90[ASN][1000 genomes]
rs2714865	0.90[ASN][1000 genomes]
rs2714866	0.90[ASN][1000 genomes]
rs2714867	0.89[ASN][1000 genomes]
rs2714868	0.90[ASN][1000 genomes]
rs2714869	0.89[ASN][1000 genomes]
rs2714870	0.90[ASN][1000 genomes]
rs2714872	0.80[ASN][1000 genomes]
rs2714875	0.91[EUR][1000 genomes]
rs2714876	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2714877	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2723494	0.91[EUR][1000 genomes]
rs2723496	0.89[EUR][1000 genomes]
rs2723497	0.89[EUR][1000 genomes]
rs2723498	0.89[EUR][1000 genomes]
rs2723499	0.89[EUR][1000 genomes]
rs2723500	0.89[EUR][1000 genomes]
rs2723501	0.90[EUR][1000 genomes]
rs2723502	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2723503	0.89[EUR][1000 genomes]
rs2723504	0.90[EUR][1000 genomes]
rs2723505	0.90[EUR][1000 genomes]
rs2723506	0.88[EUR][1000 genomes]
rs2723507	0.88[EUR][1000 genomes]
rs2723508	0.88[EUR][1000 genomes]
rs2723515	0.90[EUR][1000 genomes]
rs2723540	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2723545	0.91[EUR][1000 genomes]
rs2723552	0.91[EUR][1000 genomes]
rs2723553	0.87[EUR][1000 genomes]
rs2723554	0.89[EUR][1000 genomes]
rs2723555	0.90[EUR][1000 genomes]
rs2723556	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2723562	0.90[EUR][1000 genomes]
rs2723567	0.97[EUR][1000 genomes]
rs2723569	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2723570	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2723571	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2723572	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35819944	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4316058	0.89[EUR][1000 genomes]
rs4532510	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4543433	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4719525	0.85[ASN][1000 genomes]
rs4721661	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4721665	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4721671	0.84[ASN][1000 genomes]
rs56287412	0.88[ASN][1000 genomes]
rs67452591	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6953831	0.86[EUR][1000 genomes]
rs6955984	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958131	0.83[EUR][1000 genomes]
rs6958211	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6973480	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6978097	0.87[EUR][1000 genomes]
rs6978103	0.85[EUR][1000 genomes]
rs949451	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9942602	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs998342	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021524	chr7:17251148-17963307	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv533938	chr7:17254118-18040301	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1024398	chr7:17630148-18545073	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
4	nsv538764	chr7:17630148-18545073	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
5	nsv830913	chr7:17848480-18034218	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1026629	chr7:17862477-18362404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1025023	chr7:17865796-18357630	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1030201	chr7:17898410-18491985	Enhancers Strong transcription Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
9	nsv887808	chr7:17920613-18150005	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1018517	chr7:17926468-18127372	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv606357	chr7:17938491-18375245	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:17900400-17956600	Weak transcription	A549	lung
2	chr7:17901400-17946200	Weak transcription	NHLF	lung
3	chr7:17903400-17942400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:17903600-17945400	Weak transcription	Aorta	Aorta
5	chr7:17903600-17953000	Weak transcription	Thymus	Thymus
6	chr7:17903800-17949000	Weak transcription	NHEK	skin
7	chr7:17907200-17941000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr7:17907200-17954800	Weak transcription	Spleen	Spleen
9	chr7:17907400-17942400	Weak transcription	Small Intestine	intestine
10	chr7:17911400-17977400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:17911600-17942400	Weak transcription	HepG2	liver
12	chr7:17911800-17942400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:17913000-17955800	Weak transcription	K562	blood
14	chr7:17916200-17942600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr7:17918200-17948000	Weak transcription	GM12878-XiMat	blood
16	chr7:17918800-17942600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:17923000-17940800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr7:17923000-17942400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:17926200-17942400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr7:17926800-17941000	Weak transcription	Fetal Brain Female	brain
21	chr7:17927200-17944600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr7:17927200-17955000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:17928200-17946800	Weak transcription	Hela-S3	cervix
24	chr7:17929200-17941000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr7:17929200-17942400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr7:17929200-17951400	Weak transcription	Fetal Intestine Large	intestine
27	chr7:17929200-17952200	Weak transcription	Fetal Muscle Leg	muscle
28	chr7:17929400-17943000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:17929800-17943400	Weak transcription	Primary T cells from cord blood	blood
30	chr7:17929800-17944200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr7:17929800-17946600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr7:17929800-17948000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr7:17929800-17949200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:17929800-17951600	Weak transcription	Fetal Thymus	thymus
35	chr7:17929800-17954000	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr7:17930000-17942000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr7:17930000-17942400	Weak transcription	Liver	Liver
38	chr7:17930000-17943000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr7:17930000-17948200	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr7:17930000-17949200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:17930000-17950200	Weak transcription	Primary hematopoietic stem cells	blood
42	chr7:17930000-17950200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr7:17930000-17952400	Weak transcription	Primary B cells from peripheral blood	blood
44	chr7:17930200-17941200	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:17930200-17941200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:17930200-17941200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr7:17930200-17942600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr7:17930200-17946800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:17930200-17950200	Weak transcription	NHDF-Ad	bronchial
50	chr7:17930200-17951800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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