Variant report

Variant	rs684045
Chromosome Location	chr1:210505199-210505200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:210497683..210507034-chr1:210544536..210549319,22	MCF-7	breast:
2	chr1:210499363..210504206-chr1:210504461..210511314,11	MCF-7	breast:
3	chr1:210503754..210505570-chr1:210544608..210547185,2	MCF-7	breast:
4	chr1:210498648..210506320-chr1:210545155..210548300,7	K562	blood:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction
ENSG00000054392	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12144593	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890302	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1999890	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2357432	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357433	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765871	0.80[CHD][hapmap]
rs4292962	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56393518	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs589027	0.95[MKK][hapmap]
rs591238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs613047	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs624600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs664614	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6688459	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs684767	1.00[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap]
rs688585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs694602	0.88[EUR][1000 genomes];0.90[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	nsv8769	chr1:210403509-210564588	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs684045	TRAF3IP3	cis	cerebellum	SCAN
rs684045	HHAT	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210503000-210505600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:210503000-210506000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:210503200-210505400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:210503200-210505600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:210503200-210506400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr1:210503200-210506600	Enhancers	Fetal Heart	heart
7	chr1:210503200-210507200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:210503200-210507400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr1:210503200-210516800	Weak transcription	Lung	lung
10	chr1:210503400-210505200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:210503400-210505400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:210503400-210505600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr1:210503600-210505400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:210503600-210546800	Weak transcription	Fetal Intestine Small	intestine
15	chr1:210503800-210505200	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:210503800-210505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr1:210504000-210505400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:210504000-210505600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:210504000-210505600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:210504000-210505600	Weak transcription	Fetal Thymus	thymus
21	chr1:210504000-210506400	Weak transcription	Dnd41	blood
22	chr1:210504200-210505200	Weak transcription	Thymus	Thymus
23	chr1:210504200-210505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:210504200-210505600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr1:210504200-210505600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr1:210504200-210505600	Weak transcription	NHEK	skin
27	chr1:210504200-210505800	Weak transcription	HMEC	breast
28	chr1:210504200-210506000	Weak transcription	Left Ventricle	heart
29	chr1:210504200-210508200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:210504200-210512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:210504400-210505600	Enhancers	GM12878-XiMat	blood
32	chr1:210504400-210507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr1:210504400-210514800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:210504400-210516400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:210504600-210507600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:210504800-210506600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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