Variant report

Variant	rs2631768
Chromosome Location	chr4:8473050-8473051
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	chr4:8472459-8473558	A549	lung:	n/a	n/a
2	POLR2A	chr4:8470406-8476371	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:8472717..8474725-chr4:8621251..8624026,2	K562	blood:
2	chr4:8472049..8473735-chr4:8474244..8476711,2	K562	blood:
3	chr4:8473000..8473785-chr4:8548526..8549174,2	MCF-7	breast:
4	chr4:8471024..8473735-chr4:8474244..8476611,2	K562	blood:

Variant related genes	Relation type
TRMT44	TF binding region
ENSG00000155275	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1880024	0.81[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs2255501	0.97[ASN][1000 genomes]
rs2386227	0.83[EUR][1000 genomes]
rs2631735	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2631736	0.85[EUR][1000 genomes]
rs2631742	0.84[EUR][1000 genomes]
rs2631754	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2631762	0.83[EUR][1000 genomes]
rs2688219	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs2688227	0.83[EUR][1000 genomes]
rs2688231	0.83[EUR][1000 genomes]
rs2688235	0.86[EUR][1000 genomes]
rs2688243	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs2688247	0.84[EUR][1000 genomes]
rs3103067	0.81[ASW][hapmap]
rs4696828	0.81[CEU][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs6845969	0.80[TSI][hapmap]
rs871768	0.86[EUR][1000 genomes]
rs940133	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs940134	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs940136	0.81[CEU][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv878604	chr4:8315938-8618916	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1002680	chr4:8357163-8721214	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv829854	chr4:8402921-8506407	Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv964737	chr4:8467874-8473530	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2631768	RP11-689P11.2	cis	lung	GTEx
rs2631768	RP11-689P11.2	cis	Nerve Tibial	GTEx
rs2631768	TRMT44	cis	Nerve Tibial	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:8446400-8473800	Strong transcription	Fetal Stomach	stomach
2	chr4:8446600-8473400	Strong transcription	Dnd41	blood
3	chr4:8446600-8474000	Strong transcription	Fetal Muscle Leg	muscle
4	chr4:8447000-8474400	Strong transcription	Fetal Brain Female	brain
5	chr4:8447000-8475200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:8447000-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:8447200-8480200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:8447400-8474000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr4:8447400-8482200	Strong transcription	Primary T cells from cord blood	blood
10	chr4:8447600-8473400	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr4:8451200-8473600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:8459400-8474000	Strong transcription	Fetal Intestine Small	intestine
13	chr4:8459800-8478800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr4:8463400-8473800	Weak transcription	Fetal Kidney	kidney
15	chr4:8463800-8478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:8464600-8473200	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:8464600-8474000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:8464800-8473400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:8464800-8473600	Strong transcription	Brain Angular Gyrus	brain
20	chr4:8465200-8473600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:8465200-8474000	Strong transcription	Lung	lung
22	chr4:8465200-8482200	Strong transcription	Brain Germinal Matrix	brain
23	chr4:8465400-8473400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:8465400-8473400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr4:8465400-8473400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr4:8465400-8473400	Strong transcription	Esophagus	oesophagus
27	chr4:8465400-8473800	Strong transcription	Fetal Intestine Large	intestine
28	chr4:8465400-8473800	Strong transcription	Pancreas	Pancrea
29	chr4:8465400-8473800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr4:8465400-8474200	Strong transcription	Gastric	stomach
31	chr4:8465400-8474200	Strong transcription	Spleen	Spleen
32	chr4:8465400-8480200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr4:8465600-8473400	Strong transcription	Brain Anterior Caudate	brain
34	chr4:8465800-8474000	Strong transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:8465800-8474200	Strong transcription	Thymus	Thymus
36	chr4:8466600-8474200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:8466600-8474200	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr4:8466800-8473400	Strong transcription	NHLF	lung
39	chr4:8466800-8473600	Strong transcription	Right Ventricle	heart
40	chr4:8467000-8473400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr4:8467600-8473800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:8467600-8475800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr4:8467600-8482200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr4:8467800-8474200	Weak transcription	HSMM	muscle
45	chr4:8467800-8480400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr4:8468000-8478600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:8468400-8479600	Weak transcription	Psoas Muscle	Psoas
48	chr4:8469000-8473200	Weak transcription	Colonic Mucosa	Colon
49	chr4:8469600-8473200	Strong transcription	H9 Cell Line	embryonic stem cell
50	chr4:8469600-8473200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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