Variant report

Variant	rs2228213
Chromosome Location	chr6:12124855-12124856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAFK	chr6:12124726-12125182	HepG2	liver:	n/a	n/a
2	POLR2A	chr6:12124839-12124964	GM12878	blood:	n/a	n/a
3	MAFF	chr6:12124779-12125081	HepG2	liver:	n/a	n/a
4	MAFK	chr6:12124645-12125166	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:12124428-12124992	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:12124845-12124961	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:12124826-12127028	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:12124805-12124975	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr6:12124795-12124991	GM12878	blood:	n/a	n/a
10	POLR2A	chr6:12124706-12125127	GM12891	blood:	n/a	n/a
11	POLR2A	chr6:12124691-12125129	GM12892	blood:	n/a	n/a
12	POLR2A	chr6:12124768-12125498	GM12892	blood:	n/a	n/a
13	POLR2A	chr6:12120206-12127200	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:12122965..12125225-chr6:12131203..12132962,2	MCF-7	breast:
2	chr6:12110770..12113463-chr6:12121895..12124964,3	K562	blood:

Variant related genes	Relation type
HIVEP1	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10947758	0.87[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10947793	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12199075	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12210300	0.83[JPT][hapmap]
rs12213070	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193986	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13206426	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13209918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1998528	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2228215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3777755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777776	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3822925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4377779	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4467770	0.94[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4714201	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4714232	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6939913	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs7383768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7752678	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296258	0.94[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs9357299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366985	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369076	0.88[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.82[ASN][1000 genomes]
rs9369083	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9369108	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9380781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380859	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9394538	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9394569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

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	nsv870443	chr6:12096356-12125998	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2228213	C6orf218	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12091000-12130600	Weak transcription	Psoas Muscle	Psoas
2	chr6:12116000-12128000	Weak transcription	Fetal Heart	heart
3	chr6:12117200-12136800	Weak transcription	Brain Cingulate Gyrus	brain
4	chr6:12118400-12138400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr6:12118800-12131400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:12119200-12125000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:12119400-12126000	Strong transcription	Fetal Muscle Leg	muscle
8	chr6:12119400-12126200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:12119400-12129800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr6:12119600-12126800	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr6:12119800-12138800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr6:12120000-12128800	Strong transcription	Liver	Liver
13	chr6:12120200-12125000	Strong transcription	Fetal Intestine Large	intestine
14	chr6:12120200-12125200	Strong transcription	Fetal Muscle Trunk	muscle
15	chr6:12120200-12126000	Strong transcription	Left Ventricle	heart
16	chr6:12120200-12126000	Strong transcription	HUVEC	blood vessel
17	chr6:12120200-12129000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr6:12120400-12125000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr6:12120400-12125000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr6:12120400-12125000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr6:12120400-12125000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:12120400-12125200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:12120400-12125200	Strong transcription	NHEK	skin
24	chr6:12120400-12125400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:12120400-12126000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:12120400-12126000	Strong transcription	HepG2	liver
27	chr6:12120400-12126200	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr6:12120400-12126600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:12120400-12128200	Strong transcription	HSMM	muscle
30	chr6:12120400-12129000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr6:12121400-12128000	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr6:12121400-12128000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr6:12121400-12150200	Weak transcription	Fetal Brain Male	brain
34	chr6:12121600-12136800	Weak transcription	Hela-S3	cervix
35	chr6:12122000-12125200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr6:12122000-12134600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:12122000-12136600	Weak transcription	Osteobl	bone
38	chr6:12122000-12138200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr6:12122200-12125400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr6:12122200-12128400	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr6:12122200-12132200	Weak transcription	A549	lung
42	chr6:12122200-12132200	Weak transcription	NHLF	lung
43	chr6:12122200-12137600	Weak transcription	Brain Anterior Caudate	brain
44	chr6:12122200-12137600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:12122200-12137600	Weak transcription	Brain Substantia Nigra	brain
46	chr6:12122200-12137800	Weak transcription	HMEC	breast
47	chr6:12122200-12138600	Weak transcription	Colonic Mucosa	Colon
48	chr6:12122200-12138600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr6:12122200-12138600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr6:12122200-12138800	Weak transcription	Ovary	ovary

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