Variant report

Variant	rs4669401
Chromosome Location	chr2:9765323-9765324
allele	A/C
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	chr2:9765265-9765370	A549	lung:	n/a	n/a
2	POLR2A	chr2:9765211-9766017	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr2:9765279-9765447	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:9730968..9733407-chr2:9764631..9766138,2	MCF-7	breast:

Variant related genes	Relation type
YWHAQ	TF binding region

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10929591	0.84[ASN][1000 genomes]
rs11888902	0.86[EUR][1000 genomes]
rs11902431	0.97[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12465158	0.90[EUR][1000 genomes]
rs12470619	0.93[EUR][1000 genomes]
rs12476008	0.88[EUR][1000 genomes]
rs1524667	0.84[ASN][1000 genomes]
rs16867062	0.92[EUR][1000 genomes]
rs16867073	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16867074	0.88[EUR][1000 genomes]
rs41308184	0.93[EUR][1000 genomes]
rs4668625	0.84[ASN][1000 genomes]
rs62119390	0.90[EUR][1000 genomes]
rs62119425	0.95[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62119430	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6715408	0.93[EUR][1000 genomes]
rs6720625	0.85[ASN][1000 genomes]
rs7597961	0.90[EUR][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	nsv580915	chr2:9308148-9844178	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4669401	LOC645233///LOC732360///TDG	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9696800-9767600	Weak transcription	Gastric	stomach
2	chr2:9744800-9766800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:9748600-9765600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr2:9748600-9766600	Weak transcription	Aorta	Aorta
5	chr2:9748600-9767600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:9749000-9769200	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:9749200-9768000	Weak transcription	Stomach Mucosa	stomach
8	chr2:9749600-9768200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:9752200-9768200	Weak transcription	Colonic Mucosa	Colon
10	chr2:9753000-9767000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:9753200-9767000	Weak transcription	Spleen	Spleen
12	chr2:9754000-9767200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:9754200-9767600	Weak transcription	Esophagus	oesophagus
14	chr2:9754200-9768800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:9755000-9765600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:9755400-9765600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr2:9756200-9767800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:9756400-9767200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:9757800-9767400	Weak transcription	Placenta	Placenta
20	chr2:9758000-9767000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr2:9758000-9769400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:9758800-9767000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:9759000-9765600	Weak transcription	GM12878-XiMat	blood
24	chr2:9759000-9767000	Weak transcription	NHLF	lung
25	chr2:9760200-9765600	Weak transcription	Liver	Liver
26	chr2:9760200-9767200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr2:9760400-9767000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr2:9760400-9767000	Strong transcription	HSMM	muscle
29	chr2:9760400-9768000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr2:9760800-9765600	Weak transcription	Fetal Kidney	kidney
31	chr2:9760800-9767600	Strong transcription	Fetal Thymus	thymus
32	chr2:9761000-9767600	Weak transcription	HSMMtube	muscle
33	chr2:9761200-9765600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:9761200-9765600	Weak transcription	Brain Anterior Caudate	brain
35	chr2:9761200-9765600	Genic enhancers	Dnd41	blood
36	chr2:9761200-9765800	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:9761200-9767200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr2:9761400-9765600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr2:9761400-9766200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:9761400-9767000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:9761600-9768800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr2:9761800-9769400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:9762000-9765600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:9762000-9766400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:9762200-9765800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:9762400-9765800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:9762400-9767000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr2:9762400-9767000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:9762600-9765800	Strong transcription	NH-A	brain
50	chr2:9762600-9767400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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