Variant report

Variant	rs10429259
Chromosome Location	chr7:117512438-117512439
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	chr7:117511849-117513881	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr7:117511930-117514238	H1-neurons	neurons:	n/a	chr7:117512933-117512946 chr7:117512936-117512949 chr7:117512478-117512486 chr7:117512210-117512223 chr7:117513746-117513759 chr7:117513552-117513561
3	ZNF263	chr7:117511757-117513155	HEK293-T-REx	kidney:	n/a	chr7:117512184-117512193 chr7:117512183-117512204
4	BACH1	chr7:117512254-117513144	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr7:117512346-117513190	H1-hESC	embryonic stem cell:	n/a	n/a
6	CHD2	chr7:117512348-117512845	H1-hESC	embryonic stem cell:	n/a	chr7:117512419-117512429
7	SIN3A	chr7:117511778-117514020	H1-hESC	embryonic stem cell:	n/a	chr7:117512210-117512223 chr7:117512933-117512946
8	POLR2A	chr7:117512160-117512556	H1-hESC	embryonic stem cell:	n/a	n/a
9	TBP	chr7:117512155-117512649	H1-hESC	embryonic stem cell:	n/a	n/a
10	TAF1	chr7:117512244-117513183	H1-neurons	neurons:	n/a	n/a
11	POLR2A	chr7:117512182-117513971	H1-neurons	neurons:	n/a	n/a
12	TAF1	chr7:117512203-117512680	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr7:117512400-117512550	HA-sp	spinal cord:	n/a	n/a
14	POLR2A	chr7:117512036-117513135	SK-N-MC	brain:	n/a	n/a
15	CTBP2	chr7:117511981-117514002	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr7:117512031-117514060	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
CTTNBP2	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10428901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953856	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12113597	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532378	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12667491	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17140462	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17140498	0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2160556	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs34401510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35811430	0.93[ASN][1000 genomes]
rs4730808	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730809	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117509800-117514400	Active TSS	Brain Anterior Caudate	brain
2	chr7:117510200-117513200	Active TSS	Fetal Brain Male	brain
3	chr7:117510200-117514200	Active TSS	Brain Angular Gyrus	brain
4	chr7:117510200-117514200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr7:117510400-117514200	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr7:117510400-117514200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr7:117510800-117513800	Active TSS	Brain Cingulate Gyrus	brain
8	chr7:117510800-117514200	Active TSS	Brain Substantia Nigra	brain
9	chr7:117511000-117514200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr7:117511400-117513800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
11	chr7:117511400-117514000	Active TSS	NHLF	lung
12	chr7:117511600-117512600	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
13	chr7:117511600-117514200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
14	chr7:117511600-117514200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr7:117511600-117514400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr7:117511800-117512600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:117511800-117512800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr7:117511800-117512800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
19	chr7:117511800-117512800	Active TSS	Colonic Mucosa	Colon
20	chr7:117511800-117513000	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr7:117511800-117513200	Flanking Active TSS	Adipose Nuclei	Adipose
22	chr7:117511800-117513200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
23	chr7:117511800-117514000	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr7:117511800-117514000	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr7:117511800-117514000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr7:117511800-117514200	Active TSS	Brain Hippocampus Middle	brain
27	chr7:117511800-117514400	Active TSS	H9 Cell Line	embryonic stem cell
28	chr7:117512000-117512600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr7:117512000-117512600	Flanking Active TSS	Fetal Stomach	stomach
30	chr7:117512000-117513000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr7:117512000-117513000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:117512000-117513000	Flanking Active TSS	NH-A	brain
33	chr7:117512000-117513800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr7:117512000-117513800	Active TSS	Esophagus	oesophagus
35	chr7:117512000-117514000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr7:117512000-117514000	Active TSS	Colon Smooth Muscle	Colon
37	chr7:117512000-117514200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:117512000-117514200	Active TSS	Ovary	ovary
39	chr7:117512000-117514200	Active TSS	Right Atrium	heart
40	chr7:117512200-117512600	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
41	chr7:117512200-117512600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:117512200-117512600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr7:117512200-117512800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr7:117512200-117512800	Active TSS	Gastric	stomach
45	chr7:117512200-117512800	Flanking Active TSS	HMEC	breast
46	chr7:117512200-117513000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:117512200-117513000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr7:117512200-117513000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr7:117512200-117513000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
50	chr7:117512200-117513000	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine

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