Variant report

Variant	rs6549200
Chromosome Location	chr3:69373074-69373075
allele	G/T
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	RAD21	chr3:69372998-69374079	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:69371696..69374410-chr3:69474254..69475900,2	MCF-7	breast:

Variant related genes	Relation type
FRMD4B	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11128125	0.88[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1564758	0.90[ASN][1000 genomes]
rs1976064	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs2003264	0.83[ASN][1000 genomes]
rs2005546	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs2008239	0.90[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[ASN][1000 genomes]
rs34397489	0.90[ASN][1000 genomes]
rs6549204	0.88[ASN][1000 genomes]
rs6763080	0.90[ASN][1000 genomes]
rs6774290	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.90[ASN][1000 genomes]
rs6781841	0.88[ASN][1000 genomes]
rs6802833	0.90[ASN][1000 genomes]
rs6808107	0.84[ASN][1000 genomes]
rs7610748	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7615137	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7640281	0.93[ASN][1000 genomes]
rs9820308	0.90[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[YRI][hapmap];0.96[ASN][1000 genomes]
rs9820322	0.95[ASN][1000 genomes]
rs9844501	0.87[YRI][hapmap]
rs9867072	0.87[ASN][1000 genomes]
rs9869925	0.90[CHB][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs9872564	0.90[CHB][hapmap]
rs9876410	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.83[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9882259	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876935	chr3:69307942-69401248	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1007730	chr3:69355932-69730587	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6549200	S100A12	trans	brain	seeQTL

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69350000-69374200	Weak transcription	Aorta	Aorta
2	chr3:69356000-69373200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr3:69360600-69382200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:69362600-69373200	Weak transcription	Dnd41	blood
5	chr3:69366400-69376200	Enhancers	Brain Anterior Caudate	brain
6	chr3:69366800-69378200	Enhancers	Brain Hippocampus Middle	brain
7	chr3:69367200-69378400	Enhancers	Brain Substantia Nigra	brain
8	chr3:69367400-69374800	Enhancers	Brain Angular Gyrus	brain
9	chr3:69368200-69373200	Weak transcription	Lung	lung
10	chr3:69368400-69378200	Enhancers	Brain Cingulate Gyrus	brain
11	chr3:69369000-69377600	Weak transcription	Fetal Brain Female	brain
12	chr3:69369800-69376600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:69370200-69384000	Weak transcription	Left Ventricle	heart
14	chr3:69370400-69373600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr3:69370400-69376600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:69370400-69379200	Weak transcription	Spleen	Spleen
17	chr3:69370600-69375800	Weak transcription	HUVEC	blood vessel
18	chr3:69370800-69373200	Weak transcription	Primary B cells from cord blood	blood
19	chr3:69370800-69373200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:69370800-69373400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:69370800-69373400	Weak transcription	Fetal Thymus	thymus
22	chr3:69370800-69373400	Weak transcription	GM12878-XiMat	blood
23	chr3:69370800-69373800	Weak transcription	Thymus	Thymus
24	chr3:69371000-69373800	Enhancers	Placenta	Placenta
25	chr3:69371000-69375600	Weak transcription	Fetal Lung	lung
26	chr3:69371000-69377400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:69371400-69377000	Weak transcription	Fetal Stomach	stomach
28	chr3:69371600-69375600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:69371800-69380000	Weak transcription	Fetal Heart	heart
30	chr3:69372000-69373800	Enhancers	HSMM	muscle
31	chr3:69372000-69375000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:69372200-69373200	Weak transcription	Right Atrium	heart
33	chr3:69372200-69377400	Weak transcription	Ovary	ovary
34	chr3:69372200-69403800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:69372400-69374400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr3:69372400-69377200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:69372400-69380000	Weak transcription	NHEK	skin
38	chr3:69372800-69374800	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr3:69373000-69373200	Enhancers	Fetal Muscle Leg	muscle
40	chr3:69373000-69373400	Enhancers	Adipose Nuclei	Adipose
41	chr3:69373000-69373400	Enhancers	Monocytes-CD14+_RO01746	blood
42	chr3:69373000-69373600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:69373000-69373600	Enhancers	Duodenum Mucosa	Duodenum
44	chr3:69373000-69375000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr3:69373000-69375800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr3:69373000-69376000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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