Variant report

Variant	rs4235257
Chromosome Location	chr4:8293398-8293399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:8292974..8294945-chr4:8297191..8300156,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs13132047	0.84[MEX][hapmap]
rs13132711	0.82[CHB][hapmap];0.84[MEX][hapmap]
rs4263384	0.82[CHB][hapmap]
rs4696791	0.82[CHB][hapmap]
rs4696793	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	nsv1002794	chr4:8110083-8490934	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv878595	chr4:8154534-8390646	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv878597	chr4:8171401-8294196	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829853	chr4:8172065-8320868	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv878599	chr4:8195705-8293398	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv593627	chr4:8202211-8311043	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv878600	chr4:8209447-8312158	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878601	chr4:8214767-8440951	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Genic enhancers 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 target site	19 gene(s)	inside rSNPs	diseases
9	nsv878602	chr4:8214767-8448992	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
10	nsv1009011	chr4:8225669-8424831	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv461218	chr4:8254784-8320126	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
12	nsv593628	chr4:8254784-8320126	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
13	nsv593636	chr4:8289807-8294196	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv878603	chr4:8289807-8312158	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4235257	HS3ST1	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8279000-8317200	Weak transcription	Gastric	stomach
2	chr4:8283800-8296600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:8283800-8296600	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:8283800-8297000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:8283800-8305200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr4:8284000-8293400	Weak transcription	Adipose Nuclei	Adipose
7	chr4:8284200-8296400	Weak transcription	Fetal Lung	lung
8	chr4:8285400-8296800	Weak transcription	Colonic Mucosa	Colon
9	chr4:8285800-8299400	Strong transcription	Placenta Amnion	Placenta Amnion
10	chr4:8285800-8305600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:8286000-8296600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr4:8286000-8299000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr4:8287800-8294800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:8287800-8296000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:8287800-8300600	Strong transcription	Fetal Stomach	stomach
16	chr4:8288000-8299200	Strong transcription	Fetal Muscle Leg	muscle
17	chr4:8288400-8299200	Strong transcription	Stomach Smooth Muscle	stomach
18	chr4:8288600-8307800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:8289000-8296800	Weak transcription	Left Ventricle	heart
20	chr4:8290000-8296400	Weak transcription	Fetal Heart	heart
21	chr4:8290400-8294200	Weak transcription	Fetal Intestine Large	intestine
22	chr4:8290600-8298400	Strong transcription	Ovary	ovary
23	chr4:8291000-8297200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:8291200-8300000	Strong transcription	Right Ventricle	heart
25	chr4:8291400-8299200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr4:8292600-8296800	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr4:8292800-8294000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr4:8292800-8294200	Strong transcription	Fetal Intestine Small	intestine
29	chr4:8293200-8296600	Weak transcription	Spleen	Spleen

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