Variant report

Variant	rs12624217
Chromosome Location	chr2:39997694-39997695
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39541547..39543631-chr2:39997665..39999926,2	K562	blood:
2	chr2:39975048..39977790-chr2:39997360..39998912,2	K562	blood:
3	chr2:39996045..39997746-chr3:50647710..50649775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114737	Chromatin interaction
ENSG00000011566	Chromatin interaction
ENSG00000114738	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10164984	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10169390	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10174709	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10206408	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10207589	0.88[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs10211306	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1035138	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1035139	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11124691	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11124692	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11124693	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs11684302	0.84[CEU][hapmap]
rs12470473	0.88[CEU][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12617624	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12620957	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12623462	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12623545	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12712653	0.87[CHB][hapmap];0.84[ASN][1000 genomes]
rs12712656	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13026313	0.88[CEU][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13400213	0.92[EUR][1000 genomes]
rs13401182	0.80[AMR][1000 genomes]
rs13425906	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13428837	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1548877	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17478972	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1861258	0.85[CEU][hapmap]
rs1986876	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2041735	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2058620	0.81[CEU][hapmap];0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs2110656	0.80[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs2192685	0.96[CEU][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2373688	0.80[AMR][1000 genomes]
rs2373689	0.88[CEU][hapmap];0.80[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2540226	0.81[ASN][1000 genomes]
rs2540227	0.82[ASN][1000 genomes]
rs2716730	0.84[CEU][hapmap];0.80[CHB][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35761077	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732121	0.93[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732122	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670955	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4670956	0.80[CEU][hapmap];0.80[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4670957	0.88[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4670958	0.88[CEU][hapmap];0.93[CHB][hapmap];0.87[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4670959	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59756273	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6544242	0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6719179	0.96[CEU][hapmap];0.93[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6722610	0.81[CEU][hapmap]
rs6731026	0.85[ASN][1000 genomes]
rs6731450	0.86[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs6747842	0.87[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs6750252	0.86[ASN][1000 genomes]
rs6758453	0.87[CHB][hapmap];0.84[CHD][hapmap];0.86[ASN][1000 genomes]
rs727376	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7560642	0.92[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7565954	0.87[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap]
rs7581406	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7590912	0.81[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs7591347	0.80[EUR][1000 genomes]
rs8265	0.85[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs917960	0.96[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs917962	0.81[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs917963	0.88[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9309042	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs962262	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs997976	0.88[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833870	chr2:39837022-40026024	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv833881	chr2:39914558-40067256	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv873890	chr2:39976810-40009041	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv2696	chr2:39988381-40033288	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12624217	THUMPD2	cis	cerebellum	SCAN
rs12624217	CEBPZ	cis	cerebellum	SCAN
rs12624217	PRKD3	cis	cerebellum	SCAN
rs12624217	CYP1B1	cis	parietal	SCAN
rs12624217	A2M	trans	parietal	SCAN
rs12624217	CCDC75	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39965200-40005000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:39965200-40005400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39969800-39999800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:39971000-39999800	Weak transcription	Right Ventricle	heart
5	chr2:39971600-39998800	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:39972400-39998600	Strong transcription	HMEC	breast
7	chr2:39972400-39998800	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:39973000-39998800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:39974200-39998600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr2:39975000-39998400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:39975000-39999800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:39976200-39998800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:39976800-39999000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:39978600-40000000	Weak transcription	Fetal Heart	heart
15	chr2:39983000-39999200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr2:39983600-39998600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:39983600-39999000	Strong transcription	HSMM	muscle
18	chr2:39984800-39999600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:39985000-40005000	Weak transcription	Colonic Mucosa	Colon
20	chr2:39985200-39998400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:39985200-39999600	Weak transcription	Brain Germinal Matrix	brain
22	chr2:39985200-39999600	Weak transcription	Psoas Muscle	Psoas
23	chr2:39985200-39999800	Weak transcription	Brain Substantia Nigra	brain
24	chr2:39985200-40005000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:39985400-40005200	Weak transcription	Fetal Brain Male	brain
26	chr2:39985600-40001000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr2:39985800-39999200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr2:39985800-39999400	Weak transcription	Aorta	Aorta
29	chr2:39985800-39999600	Weak transcription	Brain Angular Gyrus	brain
30	chr2:39985800-39999800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:39985800-39999800	Weak transcription	Small Intestine	intestine
32	chr2:39985800-40004800	Weak transcription	Fetal Brain Female	brain
33	chr2:39985800-40005000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr2:39985800-40005400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr2:39985800-40005400	Weak transcription	Lung	lung
36	chr2:39986000-40004200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:39986200-40004400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr2:39986800-39999400	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:39987400-39999400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr2:39987400-39999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:39987400-39999800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr2:39987400-39999800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr2:39987400-40001000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:39987400-40001000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr2:39987600-40001000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr2:39987600-40003200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:39988000-39999600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:39988000-40004400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr2:39988200-39999600	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:39990600-39998800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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