Variant report

Variant	rs2884228
Chromosome Location	chr2:173255627-173255628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12992315	0.81[EUR][1000 genomes]
rs12996569	1.00[EUR][1000 genomes]
rs13005010	1.00[EUR][1000 genomes]
rs13011908	0.93[EUR][1000 genomes]
rs17220266	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34264824	0.88[EUR][1000 genomes]
rs34412908	0.85[EUR][1000 genomes]
rs34653380	0.88[EUR][1000 genomes]
rs35160861	0.81[EUR][1000 genomes]
rs36091681	0.99[EUR][1000 genomes]
rs6727015	0.80[EUR][1000 genomes]
rs7597542	0.87[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap]

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	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2884228	ITGA6	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173239200-173260200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:173246200-173258400	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:173246200-173260200	Weak transcription	Right Atrium	heart
4	chr2:173247000-173258200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:173249800-173262600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:173250200-173260400	Weak transcription	Thymus	Thymus
7	chr2:173252200-173261400	Weak transcription	Fetal Lung	lung
8	chr2:173252400-173256200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:173252600-173256400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr2:173253600-173262000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:173254400-173255800	Enhancers	Fetal Intestine Large	intestine
12	chr2:173254400-173256000	Enhancers	Fetal Intestine Small	intestine
13	chr2:173254400-173261400	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:173254600-173256200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:173254800-173256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:173254800-173258400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr2:173254800-173258400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:173254800-173258600	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr2:173254800-173260400	Weak transcription	Left Ventricle	heart
20	chr2:173254800-173261600	Weak transcription	Lung	lung
21	chr2:173255000-173258200	Weak transcription	Adipose Nuclei	Adipose
22	chr2:173255000-173258400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr2:173255000-173260200	Weak transcription	Fetal Thymus	thymus
24	chr2:173255000-173260200	Weak transcription	Spleen	Spleen
25	chr2:173255200-173256200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr2:173255200-173258600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:173255400-173256600	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr2:173255400-173256600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:173255600-173256000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr2:173255600-173258200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:173255600-173258400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:173255600-173258400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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