Variant report

Variant	rs12203576
Chromosome Location	chr6:13293643-13293644
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13276714..13280149-chr6:13292500..13295672,4	K562	blood:
2	chr6:13288763..13290813-chr6:13291778..13294382,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112137	Chromatin interaction
ENSG00000272379	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12212533	0.86[CEU][hapmap]
rs1899262	0.82[JPT][hapmap]
rs1937767	0.91[CEU][hapmap];0.91[MEX][hapmap]
rs202020	0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs2439546	0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.83[MEX][hapmap];0.89[MKK][hapmap];0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2496141	0.82[JPT][hapmap]
rs2496143	0.89[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2496155	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs364884	0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs381134	0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs3846903	0.95[CEU][hapmap];0.88[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs384730	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs408639	0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs408923	0.89[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs412787	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs417048	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs421057	0.85[ASN][1000 genomes]
rs442614	0.86[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs446843	0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4605869	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4711958	0.95[CEU][hapmap]
rs4715202	0.95[CEU][hapmap]
rs543645	0.91[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs546520	0.91[ASN][1000 genomes]
rs561549	0.85[EUR][1000 genomes]
rs570338	0.89[CHD][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs629262	0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs629728	0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs641293	0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs641688	0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6910418	1.00[CEU][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7774863	0.86[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs878698	0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs9381915	0.86[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9473896	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9473901	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12203576	CD83	cis	parietal	SCAN
rs12203576	ERVFRDE1	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
2	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:13285400-13302400	Weak transcription	HUVEC	blood vessel
4	chr6:13287000-13303600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:13287400-13294400	Weak transcription	Fetal Kidney	kidney
6	chr6:13287800-13294200	Weak transcription	A549	lung
7	chr6:13287800-13295200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr6:13287800-13298200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr6:13288000-13294600	Weak transcription	Fetal Brain Male	brain
10	chr6:13288000-13296200	Strong transcription	Primary B cells from peripheral blood	blood
11	chr6:13288200-13294200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr6:13288200-13294200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:13288200-13295400	Weak transcription	Fetal Heart	heart
14	chr6:13288200-13296400	Strong transcription	GM12878-XiMat	blood
15	chr6:13288400-13294200	Weak transcription	Osteobl	bone
16	chr6:13288400-13294800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:13288400-13302600	Weak transcription	Hela-S3	cervix
18	chr6:13288400-13302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr6:13288600-13293800	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr6:13288600-13294200	Weak transcription	Esophagus	oesophagus
21	chr6:13288600-13295000	Strong transcription	Primary B cells from cord blood	blood
22	chr6:13288600-13295000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr6:13288600-13296400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:13288600-13302400	Strong transcription	Fetal Brain Female	brain
25	chr6:13288600-13302600	Strong transcription	Fetal Muscle Leg	muscle
26	chr6:13288600-13321000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr6:13288600-13326400	Strong transcription	Primary T cells from cord blood	blood
28	chr6:13288800-13294200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr6:13289000-13295800	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:13289000-13299800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:13289200-13294000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr6:13289200-13294200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:13289600-13294600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:13289800-13327000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:13290200-13302800	Weak transcription	NHEK	skin
36	chr6:13290400-13294200	Weak transcription	NHDF-Ad	bronchial
37	chr6:13290400-13296200	Strong transcription	Fetal Thymus	thymus
38	chr6:13290400-13296800	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr6:13290400-13310400	Strong transcription	Dnd41	blood
40	chr6:13290600-13294200	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr6:13290600-13295600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:13290600-13296800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr6:13290600-13302800	Weak transcription	Stomach Mucosa	stomach
44	chr6:13290800-13294200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr6:13290800-13296400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr6:13291000-13295800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr6:13291000-13297200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr6:13291000-13297400	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr6:13291000-13302800	Strong transcription	Fetal Stomach	stomach
50	chr6:13291200-13303000	Strong transcription	Fetal Intestine Small	intestine

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