Variant report

Variant	rs58904113
Chromosome Location	chr3:194818430-194818431
allele	C/T
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	ZBTB7A	chr3:194818424-194818605	K562	blood:	n/a	n/a
2	ELF1	chr3:194818298-194818890	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194817020..194819382-chr3:194820062..194821788,3	K562	blood:
2	chr3:194817667..194819291-chr3:194820083..194822467,2	MCF-7	breast:

Variant related genes	Relation type
XXYLT1	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs55989369	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56765751	0.89[EUR][1000 genomes]
rs56869746	0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56879987	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6783258	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6792778	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800649	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73056521	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9851581	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9851595	0.82[ASN][1000 genomes]
rs9851740	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9857586	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867726	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	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
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
12	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:194808400-194823000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:194808600-194823000	Weak transcription	K562	blood
6	chr3:194808600-194827000	Weak transcription	Fetal Brain Female	brain
7	chr3:194808800-194821400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:194808800-194824800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:194814400-194823000	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:194814600-194827800	Enhancers	Fetal Heart	heart
11	chr3:194815000-194819600	Enhancers	Fetal Thymus	thymus
12	chr3:194815200-194818600	Weak transcription	Dnd41	blood
13	chr3:194815200-194826800	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:194815400-194821000	Weak transcription	Esophagus	oesophagus
15	chr3:194815400-194821600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:194815400-194827000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:194815600-194820800	Weak transcription	Hela-S3	cervix
18	chr3:194815800-194824400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:194815800-194827000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:194815800-194830200	Weak transcription	Primary T cells from cord blood	blood
21	chr3:194816000-194823000	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:194816000-194826800	Weak transcription	Fetal Stomach	stomach
23	chr3:194816000-194830000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:194816200-194819400	Weak transcription	Placenta	Placenta
25	chr3:194816200-194823000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:194816200-194823600	Enhancers	Primary B cells from peripheral blood	blood
27	chr3:194816200-194824000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr3:194816200-194825000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:194816400-194819800	Weak transcription	Spleen	Spleen
30	chr3:194816400-194821000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:194816400-194821000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr3:194816400-194821600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:194816400-194823000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:194816400-194823600	Weak transcription	HSMMtube	muscle
35	chr3:194816400-194825000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr3:194816400-194827000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:194816600-194826800	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:194816800-194819400	Enhancers	NHEK	skin
39	chr3:194816800-194821400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:194816800-194824200	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:194817000-194818600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr3:194817000-194819800	Weak transcription	Aorta	Aorta
43	chr3:194817000-194820800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:194817200-194819400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:194817200-194820800	Weak transcription	Lung	lung
46	chr3:194817200-194823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:194817200-194831200	Weak transcription	Gastric	stomach
48	chr3:194817400-194818800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr3:194817400-194820000	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:194817400-194823000	Weak transcription	Fetal Intestine Small	intestine

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