Variant report

Variant	rs828895
Chromosome Location	chr2:74339310-74339311
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:74225365..74228086-chr2:74337531..74340333,2	K562	blood:
2	chr2:74335291..74341165-chr2:74346061..74348984,7	K562	blood:
3	chr2:74336985..74342809-chr2:74343895..74348590,10	MCF-7	breast:
4	chr2:74207099..74209137-chr2:74336774..74339550,2	MCF-7	breast:
5	chr2:74210918..74213752-chr2:74338111..74340312,2	MCF-7	breast:
6	chr2:74336308..74342547-chr2:74345865..74348984,6	K562	blood:
7	chr2:74335713..74338068-chr2:74339184..74340724,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235499	Chromatin interaction
ENSG00000257800	Chromatin interaction
ENSG00000255989	Chromatin interaction
ENSG00000237883	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs17009632	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs41285981	1.00[EUR][1000 genomes]
rs41285983	1.00[EUR][1000 genomes]
rs57498180	1.00[EUR][1000 genomes]
rs59253442	1.00[EUR][1000 genomes]
rs61120808	1.00[EUR][1000 genomes]
rs6731282	1.00[CEU][hapmap]
rs6745776	1.00[GIH][hapmap]
rs72909178	0.94[EUR][1000 genomes]
rs72909198	1.00[EUR][1000 genomes]
rs72915079	1.00[EUR][1000 genomes]
rs72915085	1.00[EUR][1000 genomes]
rs828894	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs831526	1.00[CEU][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
rs828895	GDPD5	trans	brain	seeQTL
rs828895	TMEM74	trans	brain	seeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74322200-74346600	Weak transcription	Hela-S3	cervix
2	chr2:74328600-74339400	Weak transcription	Stomach Mucosa	stomach
3	chr2:74329600-74347000	Weak transcription	HSMMtube	muscle
4	chr2:74330200-74347000	Weak transcription	Aorta	Aorta
5	chr2:74330400-74346800	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr2:74330600-74341000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:74330600-74341200	Weak transcription	Spleen	Spleen
8	chr2:74330600-74346600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:74330600-74347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:74330600-74347000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr2:74330600-74347000	Weak transcription	Pancreas	Pancrea
12	chr2:74330800-74346800	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:74330800-74347000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:74331000-74340400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:74331200-74347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:74332000-74342000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr2:74332000-74346400	Weak transcription	Dnd41	blood
18	chr2:74332000-74346800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:74332600-74339600	Weak transcription	Fetal Intestine Large	intestine
20	chr2:74332600-74346400	Weak transcription	GM12878-XiMat	blood
21	chr2:74332600-74347000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:74332600-74347000	Weak transcription	Esophagus	oesophagus
23	chr2:74332800-74346800	Weak transcription	NHEK	skin
24	chr2:74333000-74346800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr2:74333200-74346800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr2:74333200-74347000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:74333600-74346600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:74334600-74340000	Weak transcription	Fetal Thymus	thymus
29	chr2:74335600-74346800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:74336000-74347000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr2:74336200-74346600	Weak transcription	Primary T cells from cord blood	blood
32	chr2:74336200-74346600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr2:74339000-74339400	Enhancers	K562	blood

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