Variant report

Variant	rs2410840
Chromosome Location	chr3:194983053-194983054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:194978839-194983234	HUVEC	blood vessel:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:194974867..194977335-chr3:194981493..194983475,2	K562	blood:
2	chr3:194404889..194408128-chr3:194979816..194983069,5	MCF-7	breast:
3	chr3:194978258..194982064-chr3:194982349..194986625,5	MCF-7	breast:
4	chr3:194390925..194393722-chr3:194982636..194985275,2	MCF-7	breast:
5	chr3:194391105..194394740-chr3:194978001..194983059,6	K562	blood:
6	chr3:194391105..194394913-chr3:194978195..194983059,8	K562	blood:
7	chr3:194980181..194984046-chr3:195161738..195167079,6	K562	blood:
8	chr3:194979343..194985907-chr3:194989595..194992143,7	K562	blood:
9	chr3:194979343..194983092-chr3:194989595..194993137,5	K562	blood:

No data

Variant related genes	Relation type
XXYLT1	TF binding region
ENSG00000114331	Chromatin interaction
ENSG00000185112	Chromatin interaction
ENSG00000041802	Chromatin interaction
ENSG00000173950	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10933706	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11718218	0.81[ASN][1000 genomes]
rs13062574	1.00[ASN][1000 genomes]
rs1832667	0.87[ASN][1000 genomes]
rs2050809	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2050810	0.88[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2410839	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28375276	0.93[ASN][1000 genomes]
rs28688106	0.80[ASN][1000 genomes]
rs3087885	0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3773418	0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs4677671	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4677820	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677825	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4677830	1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs58204696	0.93[ASN][1000 genomes]
rs6437467	0.86[ASN][1000 genomes]
rs6780743	0.93[ASN][1000 genomes]
rs6791943	0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6792029	0.88[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6793035	1.00[JPT][hapmap]
rs6795263	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6798243	0.90[YRI][hapmap]
rs73080837	0.86[ASN][1000 genomes]
rs73080839	0.86[ASN][1000 genomes]
rs752206	0.82[EUR][1000 genomes]
rs7610022	0.93[ASN][1000 genomes]
rs7612694	0.86[ASN][1000 genomes]
rs7638924	0.86[ASN][1000 genomes]
rs7640100	0.84[ASN][1000 genomes]
rs7643947	0.86[ASN][1000 genomes]
rs7644002	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs7649142	0.93[ASN][1000 genomes]
rs823297	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs823298	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs823299	0.86[ASN][1000 genomes]
rs823303	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs823304	0.93[ASN][1000 genomes]
rs823305	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs823307	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs823308	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs823309	0.93[ASN][1000 genomes]
rs823312	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs823313	0.86[ASN][1000 genomes]
rs9288747	0.80[ASN][1000 genomes]
rs9831944	0.86[ASN][1000 genomes]
rs9832920	0.93[ASN][1000 genomes]
rs9860389	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9863901	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9870813	1.00[JPT][hapmap]
rs9878312	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv984539	chr3:194945800-194984579	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
15	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2410840	FAM43A	cis	parietal	SCAN
rs2410840	ACAP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194981400-194984400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:194981400-194987800	Weak transcription	Psoas Muscle	Psoas
3	chr3:194981400-194990000	Weak transcription	HSMMtube	muscle
4	chr3:194981400-194990800	Weak transcription	Aorta	Aorta
5	chr3:194981600-194984200	Weak transcription	NHEK	skin
6	chr3:194981600-194984800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:194981600-194984800	Weak transcription	HMEC	breast
8	chr3:194981600-194985000	Weak transcription	K562	blood
9	chr3:194981600-194986000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:194981600-194986200	Weak transcription	Hela-S3	cervix
11	chr3:194981600-194986400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:194981600-194986400	Weak transcription	Left Ventricle	heart
13	chr3:194981600-194986400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:194981600-194986800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr3:194981600-194987000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:194981600-194989600	Weak transcription	Right Ventricle	heart
17	chr3:194981600-194989800	Weak transcription	Brain Substantia Nigra	brain
18	chr3:194981600-194990000	Weak transcription	A549	lung
19	chr3:194981600-194990200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:194981600-194990200	Weak transcription	HSMM	muscle
21	chr3:194981600-194990600	Weak transcription	Ovary	ovary
22	chr3:194981800-194983800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:194981800-194983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:194981800-194984000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:194981800-194984000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:194981800-194984000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:194981800-194984200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:194981800-194984600	Weak transcription	Esophagus	oesophagus
29	chr3:194981800-194984800	Weak transcription	Fetal Stomach	stomach
30	chr3:194981800-194986000	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:194981800-194986200	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:194981800-194986200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:194981800-194986200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr3:194981800-194986200	Weak transcription	NHLF	lung
35	chr3:194981800-194986400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr3:194981800-194986600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:194981800-194986600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr3:194981800-194986800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:194981800-194987200	Weak transcription	Fetal Muscle Leg	muscle
40	chr3:194981800-194987400	Weak transcription	Brain Germinal Matrix	brain
41	chr3:194981800-194987800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:194981800-194987800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr3:194981800-194987800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr3:194981800-194989400	Weak transcription	Brain Angular Gyrus	brain
45	chr3:194981800-194989400	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:194981800-194989400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:194981800-194989600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:194981800-194989600	Weak transcription	Liver	Liver
49	chr3:194981800-194989600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr3:194981800-194989600	Weak transcription	Colon Smooth Muscle	Colon

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