Variant report

Variant	rs293800
Chromosome Location	chr3:191082835-191082836
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191080948..191083585-chr3:191091535..191093381,2	K562	blood:

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10937477	0.87[ASN][1000 genomes]
rs13061649	0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1347400	0.85[ASN][1000 genomes]
rs1465737	0.88[EUR][1000 genomes]
rs1473866	0.87[ASN][1000 genomes]
rs150506	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs159488	0.85[ASN][1000 genomes]
rs159489	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1656143	0.87[AFR][1000 genomes]
rs1662184	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs167148	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs176820	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs176821	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs176822	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs184140	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186063	0.81[CEU][hapmap]
rs186064	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186065	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs186066	0.85[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs188384	0.90[CEU][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188385	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211043	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2572064	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs293797	0.89[ASN][1000 genomes]
rs293798	0.87[ASN][1000 genomes]
rs293802	0.91[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293804	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293807	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293809	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293810	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293811	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293812	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293813	0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293814	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293815	0.89[ASN][1000 genomes]
rs293837	0.87[AFR][1000 genomes]
rs293839	0.90[YRI][hapmap];0.84[AFR][1000 genomes]
rs293840	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs293841	0.87[AFR][1000 genomes]
rs293844	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293846	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293851	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs297396	0.89[ASN][1000 genomes]
rs364519	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs366626	0.91[ASN][1000 genomes]
rs367747	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368665	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369174	1.00[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs373035	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs381090	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383075	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs383529	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs386241	0.87[AFR][1000 genomes]
rs389765	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs390744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs392311	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs399575	0.87[AFR][1000 genomes]
rs401465	0.89[ASN][1000 genomes]
rs403078	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs407226	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs415149	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs420266	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs426466	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs429374	0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs429521	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs432085	0.90[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs434556	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436393	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs436428	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs437244	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438589	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs441509	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs445914	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs447931	0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs448133	0.89[ASN][1000 genomes]
rs449398	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4677630	0.85[ASN][1000 genomes]
rs4677734	0.85[ASN][1000 genomes]
rs4677735	0.81[CEU][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs491252	0.88[AFR][1000 genomes]
rs513632	0.87[AFR][1000 genomes]
rs520494	0.87[AFR][1000 genomes]
rs520600	0.87[AFR][1000 genomes]
rs523270	0.89[ASN][1000 genomes]
rs525774	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs526785	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529523	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566548	0.91[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568702	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs578401	0.88[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6779820	0.85[ASN][1000 genomes]
rs6953	0.91[CEU][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs697905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs709142	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847278	0.82[ASN][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	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv508266	chr3:191064212-191083637	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv878107	chr3:191069984-191100073	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv592852	chr3:191073228-191093310	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv592853	chr3:191073228-191094985	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs293800	CCDC50	cis	Thyroid	GTEx
rs293800	CCDC50	cis	Artery Aorta	GTEx
rs293800	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191069800-191096000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:191071000-191088400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
4	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
5	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:191073600-191083000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:191073600-191090000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:191074600-191092800	Weak transcription	Esophagus	oesophagus
11	chr3:191074600-191094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:191074800-191083000	Strong transcription	Primary B cells from cord blood	blood
13	chr3:191074800-191085800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:191074800-191094200	Weak transcription	A549	lung
15	chr3:191075000-191097400	Weak transcription	Thymus	Thymus
16	chr3:191075200-191084200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:191075600-191083000	Strong transcription	Fetal Intestine Large	intestine
18	chr3:191075600-191084200	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr3:191075600-191084600	Strong transcription	Fetal Lung	lung
20	chr3:191075600-191087000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:191075800-191083000	Strong transcription	Rectal Mucosa Donor 31	rectum
22	chr3:191075800-191085200	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr3:191076000-191088800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr3:191076000-191092800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:191076200-191091000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:191077200-191086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr3:191077600-191084600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr3:191077600-191094200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:191078000-191084200	Strong transcription	Colon Smooth Muscle	Colon
30	chr3:191078000-191087600	Weak transcription	Psoas Muscle	Psoas
31	chr3:191078000-191089200	Strong transcription	Primary B cells from peripheral blood	blood
32	chr3:191078600-191083400	Strong transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:191079400-191093000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr3:191079400-191094200	Weak transcription	Brain Anterior Caudate	brain
35	chr3:191079400-191094800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:191079600-191083600	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:191079600-191087600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:191079600-191088800	Weak transcription	Fetal Brain Male	brain
40	chr3:191079600-191089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:191079600-191089800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:191079600-191092600	Weak transcription	Primary T cells from cord blood	blood
43	chr3:191079600-191099200	Weak transcription	Spleen	Spleen
44	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:191079600-191121200	Weak transcription	Gastric	stomach
46	chr3:191079800-191094200	Weak transcription	Brain Substantia Nigra	brain
47	chr3:191080000-191087600	Weak transcription	Fetal Kidney	kidney
48	chr3:191080200-191086800	Weak transcription	Brain Germinal Matrix	brain
49	chr3:191080200-191094600	Weak transcription	Stomach Mucosa	stomach
50	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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