Variant report

Variant	rs2788140
Chromosome Location	chr1:212104854-212104855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212102942..212105298-chr1:212120258..212122026,2	MCF-7	breast:
2	chr1:212100825..212103790-chr1:212103837..212105355,2	K562	blood:
3	chr1:212089622..212092139-chr1:212102871..212105783,2	K562	blood:
4	chr1:212071600..212073818-chr1:212104650..212107451,2	K562	blood:
5	chr1:212101758..212105730-chr1:212107353..212109879,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000233626	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1316820	0.80[ASN][1000 genomes]
rs1578992	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.80[AMR][1000 genomes]
rs1578993	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1933593	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.80[EUR][1000 genomes]
rs2014029	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2105162	0.87[ASN][1000 genomes]
rs2248191	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2358386	0.94[ASW][hapmap];0.96[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2358440	0.90[JPT][hapmap];0.86[YRI][hapmap]
rs2788133	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2788139	0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs2808385	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2808392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2884428	0.88[CHD][hapmap];0.95[JPT][hapmap]
rs2970599	0.89[ASW][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs2970601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2993528	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2993531	0.89[ASW][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap]
rs2993533	0.89[ASW][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap]
rs2993534	0.81[ASN][1000 genomes]
rs2993541	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2993544	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3009985	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3010003	0.89[ASW][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap];0.86[YRI][hapmap];0.80[ASN][1000 genomes]
rs3010004	0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs3010006	0.83[ASN][1000 genomes]
rs3010023	0.90[JPT][hapmap];0.86[YRI][hapmap]
rs3738449	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs4951435	0.80[ASN][1000 genomes]
rs59706922	0.86[ASN][1000 genomes]
rs6657728	0.88[CHD][hapmap];0.90[JPT][hapmap]
rs6684814	0.86[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2788140	MAPKAPK2	cis	parietal	SCAN
rs2788140	INTS7	Cis_1M	lymphoblastoid	RTeQTL
rs2788140	SYT14	cis	parietal	SCAN
rs2788140	PROX1	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212084800-212113000	Weak transcription	Brain Anterior Caudate	brain
2	chr1:212098800-212106000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:212100600-212109000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:212101400-212107800	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:212102000-212106200	Weak transcription	Right Atrium	heart
6	chr1:212102000-212109000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:212102400-212106200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:212102400-212107800	Weak transcription	Spleen	Spleen
9	chr1:212102400-212113200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:212102600-212115200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:212102600-212120400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:212102800-212105800	Weak transcription	HSMMtube	muscle
13	chr1:212102800-212111400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:212102800-212114400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr1:212102800-212115000	Weak transcription	Fetal Thymus	thymus
16	chr1:212102800-212115200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:212103000-212105000	Enhancers	K562	blood
18	chr1:212103000-212106000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr1:212103000-212107800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:212103000-212132600	Weak transcription	Gastric	stomach
21	chr1:212103200-212105400	Weak transcription	Primary B cells from cord blood	blood
22	chr1:212103200-212106000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:212103200-212107800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:212103200-212108600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr1:212103200-212115000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:212103200-212115000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:212103200-212115200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:212103200-212115200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr1:212103400-212105400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:212103400-212106000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr1:212103400-212106000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:212103400-212111600	Weak transcription	Liver	Liver
33	chr1:212103400-212113200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:212103400-212113200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:212103600-212105400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:212103600-212105600	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:212103600-212106000	Weak transcription	Pancreas	Pancrea
38	chr1:212103600-212106200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:212103600-212111800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr1:212103600-212111800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:212103600-212115000	Weak transcription	NHEK	skin
42	chr1:212103600-212115400	Weak transcription	HMEC	breast
43	chr1:212103600-212132200	Weak transcription	Esophagus	oesophagus
44	chr1:212103800-212132200	Weak transcription	NHLF	lung
45	chr1:212104000-212117600	Weak transcription	HepG2	liver
46	chr1:212104200-212115000	Weak transcription	Lung	lung
47	chr1:212104400-212105000	Enhancers	Fetal Muscle Leg	muscle
48	chr1:212104400-212106000	Weak transcription	Right Ventricle	heart
49	chr1:212104400-212108000	Enhancers	Fetal Muscle Trunk	muscle
50	chr1:212104600-212107800	Enhancers	GM12878-XiMat	blood

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