Variant report

Variant	rs35684403
Chromosome Location	chr2:113338149-113338150
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	POLR2A	chr2:113337771-113339003	K562	blood:	n/a	n/a
2	POLR2A	chr2:113337885-113338794	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:113238986..113241764-chr2:113336898..113340191,3	MCF-7	breast:
2	chr2:113335699..113339674-chr2:113340106..113343204,5	K562	blood:

Variant related genes	Relation type
ENSG00000207383	TF binding region
CHCHD5	TF binding region
ENSG00000125611	Chromatin interaction
ENSG00000114999	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs13015822	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13018087	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34117931	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34137042	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66571556	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874877	chr2:113287964-113382054	Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35684403	RGPD4///RGPD5///RGPD6///RGPD8	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113301200-113340200	Weak transcription	Right Atrium	heart
2	chr2:113301200-113341000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:113326400-113340200	Weak transcription	Stomach Mucosa	stomach
4	chr2:113326600-113341000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:113330400-113339800	Weak transcription	Fetal Heart	heart
6	chr2:113331400-113340800	Weak transcription	Fetal Brain Male	brain
7	chr2:113331400-113341400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:113332200-113341600	Weak transcription	Small Intestine	intestine
9	chr2:113333000-113340800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:113333000-113341000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:113333200-113339800	Weak transcription	Pancreas	Pancrea
12	chr2:113333200-113341000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:113333200-113341000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:113333200-113341000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:113333200-113341000	Weak transcription	Fetal Kidney	kidney
16	chr2:113333200-113341200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:113333200-113341200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:113333200-113341200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:113333200-113341200	Weak transcription	Lung	lung
20	chr2:113333400-113340200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:113333400-113340800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:113333400-113341000	Weak transcription	Spleen	Spleen
23	chr2:113333600-113341000	Weak transcription	Gastric	stomach
24	chr2:113333600-113341400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:113333800-113340200	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr2:113333800-113340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:113333800-113341000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr2:113333800-113341000	Weak transcription	Right Ventricle	heart
29	chr2:113334000-113339800	Weak transcription	K562	blood
30	chr2:113334000-113340200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:113334000-113340200	Weak transcription	Adipose Nuclei	Adipose
32	chr2:113334000-113340200	Weak transcription	Colon Smooth Muscle	Colon
33	chr2:113334000-113340800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr2:113334000-113341000	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr2:113334200-113339800	Weak transcription	Brain Substantia Nigra	brain
36	chr2:113334200-113340200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:113334200-113340400	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr2:113334200-113340800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:113334200-113340800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:113334200-113340800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:113334200-113340800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:113334200-113341000	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr2:113334200-113341200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr2:113334200-113341200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:113334400-113339200	Weak transcription	Thymus	Thymus
46	chr2:113334400-113339800	Weak transcription	Liver	Liver
47	chr2:113334400-113339800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:113334400-113339800	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:113334400-113339800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:113334400-113340000	Weak transcription	Primary T cells fromperipheralblood	blood

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