Variant report

Variant	rs6781643
Chromosome Location	chr3:194985678-194985679
allele	C/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	chr3:194985628-194985950	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:194978258..194982064-chr3:194982349..194986625,5	MCF-7	breast:
2	chr3:194961621..194965085-chr3:194983168..194985887,3	K562	blood:
3	chr3:194979343..194985907-chr3:194989595..194992143,7	K562	blood:
4	chr3:194384423..194386618-chr3:194984770..194986296,2	K562	blood:

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10933706	0.86[EUR][1000 genomes]
rs11718218	0.82[EUR][1000 genomes]
rs1832667	0.90[EUR][1000 genomes]
rs2050809	0.86[EUR][1000 genomes]
rs2050810	0.91[EUR][1000 genomes]
rs2410803	0.81[EUR][1000 genomes]
rs2410839	0.92[EUR][1000 genomes]
rs28375276	0.82[EUR][1000 genomes]
rs3087885	0.92[EUR][1000 genomes]
rs3773418	0.92[EUR][1000 genomes]
rs4677825	0.86[EUR][1000 genomes]
rs4677830	0.85[EUR][1000 genomes]
rs58204696	0.82[EUR][1000 genomes]
rs6437467	0.88[EUR][1000 genomes]
rs6780743	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6791601	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6791943	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6792029	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6795263	0.88[EUR][1000 genomes]
rs7610022	0.91[EUR][1000 genomes]
rs7612694	0.85[EUR][1000 genomes]
rs7638924	0.85[EUR][1000 genomes]
rs7640100	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7643947	0.82[EUR][1000 genomes]
rs7644002	0.85[EUR][1000 genomes]
rs7649142	0.89[EUR][1000 genomes]
rs823297	0.82[EUR][1000 genomes]
rs823298	0.82[EUR][1000 genomes]
rs823299	0.82[EUR][1000 genomes]
rs823303	0.82[EUR][1000 genomes]
rs823304	0.82[EUR][1000 genomes]
rs823305	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs823307	0.82[EUR][1000 genomes]
rs823308	0.82[EUR][1000 genomes]
rs823309	0.82[EUR][1000 genomes]
rs823312	0.82[EUR][1000 genomes]
rs823313	0.82[EUR][1000 genomes]
rs9832920	0.88[EUR][1000 genomes]
rs9860389	0.85[EUR][1000 genomes]
rs9863901	0.92[EUR][1000 genomes]
rs9878312	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
5	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
6	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
7	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers 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	20 gene(s)	inside rSNPs	diseases
11	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
12	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
13	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
14	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194981400-194987800	Weak transcription	Psoas Muscle	Psoas
2	chr3:194981400-194990000	Weak transcription	HSMMtube	muscle
3	chr3:194981400-194990800	Weak transcription	Aorta	Aorta
4	chr3:194981600-194986000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:194981600-194986200	Weak transcription	Hela-S3	cervix
6	chr3:194981600-194986400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:194981600-194986400	Weak transcription	Left Ventricle	heart
8	chr3:194981600-194986400	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr3:194981600-194986800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:194981600-194987000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:194981600-194989600	Weak transcription	Right Ventricle	heart
12	chr3:194981600-194989800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:194981600-194990000	Weak transcription	A549	lung
14	chr3:194981600-194990200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:194981600-194990200	Weak transcription	HSMM	muscle
16	chr3:194981600-194990600	Weak transcription	Ovary	ovary
17	chr3:194981800-194986000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:194981800-194986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:194981800-194986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:194981800-194986200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr3:194981800-194986200	Weak transcription	NHLF	lung
22	chr3:194981800-194986400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:194981800-194986600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:194981800-194986600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:194981800-194986800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:194981800-194987200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:194981800-194987400	Weak transcription	Brain Germinal Matrix	brain
28	chr3:194981800-194987800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:194981800-194987800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:194981800-194987800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr3:194981800-194989400	Weak transcription	Brain Angular Gyrus	brain
32	chr3:194981800-194989400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:194981800-194989400	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:194981800-194989600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:194981800-194989600	Weak transcription	Liver	Liver
36	chr3:194981800-194989600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr3:194981800-194989600	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:194981800-194989600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:194981800-194989600	Weak transcription	Fetal Heart	heart
40	chr3:194981800-194989600	Weak transcription	Lung	lung
41	chr3:194981800-194989600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr3:194981800-194989800	Weak transcription	Adipose Nuclei	Adipose
43	chr3:194981800-194989800	Weak transcription	Colonic Mucosa	Colon
44	chr3:194981800-194989800	Weak transcription	Fetal Brain Female	brain
45	chr3:194981800-194989800	Weak transcription	Gastric	stomach
46	chr3:194981800-194989800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr3:194981800-194989800	Weak transcription	NHDF-Ad	bronchial
48	chr3:194981800-194990000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:194981800-194990000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:194981800-194990000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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