Variant report

Variant	rs7642061
Chromosome Location	chr3:112929748-112929749
allele	A/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	CTBP2	chr3:112929701-112931583	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr3:112929650-112930052	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr3:112929109-112930171	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3AK20	chr3:112929674-112929947	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr3:112929656-112930247	H1-hESC	embryonic stem cell:	n/a	chr3:112929671-112929680 chr3:112930218-112930232
6	YY1	chr3:112929475-112930575	H1-hESC	embryonic stem cell:	n/a	chr3:112930485-112930494 chr3:112930480-112930494 chr3:112930483-112930497 chr3:112930485-112930496
7	POLR2A	chr3:112929554-112930727	H1-hESC	embryonic stem cell:	n/a	n/a
8	SIN3A	chr3:112929169-112931694	H1-hESC	embryonic stem cell:	n/a	chr3:112929815-112929828 chr3:112930962-112930971
9	ZNF143	chr3:112929476-112930608	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr3:112929536-112930294	H1-hESC	embryonic stem cell:	n/a	chr3:112929671-112929680 chr3:112930218-112930232
11	TAF1	chr3:112929338-112929837	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:112929722..112932026-chr3:112933958..112936481,2	K562	blood:
2	chr3:112929165..112932026-chr3:112933299..112935458,2	K562	blood:
3	chr3:112875811..112877981-chr3:112929321..112930900,2	MCF-7	breast:

Variant related genes	Relation type
BOC	TF binding region
ENSG00000240057	Chromatin interaction
ENSG00000144857	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1027554	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4364141	0.85[EUR][1000 genomes]
rs7621832	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3431441	chr3:112453467-113213252	Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv829677	chr3:112857075-113038987	Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1003511	chr3:112858775-112989045	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv877346	chr3:112893640-112938683	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv877347	chr3:112895679-112934752	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv877348	chr3:112914756-113012509	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	esv3394751	chr3:112928562-112932960	Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	esv3423811	chr3:112929687-112932635	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112929000-112929800	Enhancers	Pancreas	Pancrea
2	chr3:112929000-112930000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr3:112929200-112929800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:112929200-112929800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:112929200-112929800	Active TSS	Adipose Nuclei	Adipose
6	chr3:112929200-112929800	Flanking Active TSS	Colon Smooth Muscle	Colon
7	chr3:112929200-112930000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
8	chr3:112929200-112930000	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr3:112929200-112930000	Flanking Active TSS	Fetal Muscle Trunk	muscle
10	chr3:112929200-112930200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:112929200-112930200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:112929200-112930200	Bivalent/Poised TSS	Primary B cells from cord blood	blood
13	chr3:112929200-112930400	Flanking Active TSS	Fetal Muscle Leg	muscle
14	chr3:112929200-112931200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr3:112929200-112931200	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr3:112929200-112931400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr3:112929200-112931400	Bivalent/Poised TSS	Fetal Intestine Small	intestine
18	chr3:112929200-112932000	Active TSS	Fetal Kidney	kidney
19	chr3:112929200-112932400	Active TSS	Brain Anterior Caudate	brain
20	chr3:112929400-112929800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:112929400-112929800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:112929400-112929800	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:112929400-112929800	Flanking Active TSS	Esophagus	oesophagus
24	chr3:112929400-112929800	Enhancers	HSMMtube	muscle
25	chr3:112929400-112929800	Flanking Active TSS	NHEK	skin
26	chr3:112929400-112930200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:112929400-112930200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:112929400-112930200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:112929400-112930400	Active TSS	Brain Hippocampus Middle	brain
30	chr3:112929400-112931200	Active TSS	H1 Cell Line	embryonic stem cell
31	chr3:112929400-112931200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:112929400-112931200	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr3:112929400-112931200	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
34	chr3:112929400-112931400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:112929400-112931600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:112929400-112931600	Active TSS	NH-A	brain
37	chr3:112929400-112931800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:112929400-112932400	Active TSS	Brain Substantia Nigra	brain
39	chr3:112929400-112932400	Active TSS	Ovary	ovary
40	chr3:112929400-112932400	Active TSS	NHDF-Ad	bronchial
41	chr3:112929600-112929800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:112929600-112929800	Bivalent Enhancer	Fetal Brain Male	brain
43	chr3:112929600-112929800	Active TSS	Fetal Brain Female	brain
44	chr3:112929600-112929800	Active TSS	Fetal Stomach	stomach
45	chr3:112929600-112929800	Active TSS	Stomach Smooth Muscle	stomach
46	chr3:112929600-112929800	Enhancers	A549	lung
47	chr3:112929600-112929800	Active TSS	HMEC	breast
48	chr3:112929600-112930000	Active TSS	HUES6 Cell Line	embryonic stem cell
49	chr3:112929600-112930000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:112929600-112930000	Active TSS	Brain Germinal Matrix	brain

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