Variant report

Variant	rs828867
Chromosome Location	chr2:74334462-74334463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74333085..74335496-chr2:74346524..74348825,2	MCF-7	breast:
2	chr2:74211163..74212719-chr2:74332810..74334691,2	MCF-7	breast:
3	chr2:74330613..74332163-chr2:74332927..74334673,2	K562	blood:
4	chr2:74334291..74335932-chr2:74618806..74620768,2	K562	blood:

Variant related genes	Relation type
ENSG00000235499	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000204843	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10201998	0.85[YRI][hapmap]
rs1026150	0.90[JPT][hapmap]
rs1095969	0.90[JPT][hapmap]
rs13025827	0.90[JPT][hapmap]
rs1667615	0.90[JPT][hapmap]
rs1667616	0.90[JPT][hapmap]
rs1667622	0.90[JPT][hapmap]
rs4429500	0.82[JPT][hapmap]
rs4452177	0.84[JPT][hapmap]
rs6707619	0.81[JPT][hapmap]
rs6758220	0.90[JPT][hapmap]
rs702463	0.90[JPT][hapmap]
rs702464	0.90[JPT][hapmap]
rs828841	0.90[JPT][hapmap]
rs828847	0.90[JPT][hapmap]

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	nsv874284	chr2:74283728-74348797	Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv874285	chr2:74283728-74355244	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs828867	MRPL19	cis	parietal	SCAN
rs828867	MTHFD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74308400-74336200	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr2:74317200-74335000	Weak transcription	NH-A	brain
3	chr2:74322200-74346600	Weak transcription	Hela-S3	cervix
4	chr2:74328200-74335400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:74328400-74334800	Weak transcription	HMEC	breast
6	chr2:74328400-74336000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:74328400-74339000	Weak transcription	K562	blood
8	chr2:74328600-74339400	Weak transcription	Stomach Mucosa	stomach
9	chr2:74329600-74347000	Weak transcription	HSMMtube	muscle
10	chr2:74330000-74336000	Weak transcription	Colonic Mucosa	Colon
11	chr2:74330200-74347000	Weak transcription	Aorta	Aorta
12	chr2:74330400-74335600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:74330400-74335800	Weak transcription	Thymus	Thymus
14	chr2:74330400-74338000	Weak transcription	Left Ventricle	heart
15	chr2:74330400-74346800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr2:74330600-74335200	Weak transcription	Adipose Nuclei	Adipose
17	chr2:74330600-74341000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:74330600-74341200	Weak transcription	Spleen	Spleen
19	chr2:74330600-74346600	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:74330600-74347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:74330600-74347000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:74330600-74347000	Weak transcription	Pancreas	Pancrea
23	chr2:74330800-74346800	Weak transcription	Brain Hippocampus Middle	brain
24	chr2:74330800-74347000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:74331000-74335200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr2:74331000-74338800	Weak transcription	Brain Substantia Nigra	brain
27	chr2:74331000-74340400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr2:74331200-74336000	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:74331200-74338800	Weak transcription	Primary B cells from cord blood	blood
30	chr2:74331200-74347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:74331400-74335000	Weak transcription	Liver	Liver
32	chr2:74332000-74334600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:74332000-74335200	Weak transcription	HepG2	liver
34	chr2:74332000-74342000	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:74332000-74346400	Weak transcription	Dnd41	blood
36	chr2:74332000-74346800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr2:74332200-74335800	Weak transcription	Brain Germinal Matrix	brain
38	chr2:74332400-74336400	Weak transcription	Fetal Intestine Small	intestine
39	chr2:74332400-74336800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr2:74332400-74338200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr2:74332600-74335600	Weak transcription	Primary T cells from cord blood	blood
42	chr2:74332600-74339600	Weak transcription	Fetal Intestine Large	intestine
43	chr2:74332600-74346400	Weak transcription	GM12878-XiMat	blood
44	chr2:74332600-74347000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:74332600-74347000	Weak transcription	Esophagus	oesophagus
46	chr2:74332800-74334600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr2:74332800-74346800	Weak transcription	NHEK	skin
48	chr2:74333000-74335200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:74333000-74336600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr2:74333000-74346800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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