Variant report

Variant	rs843743
Chromosome Location	chr2:54501025-54501026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54501016..54503842-chr2:54504791..54507736,2	MCF-7	breast:
2	chr2:54495606..54497945-chr2:54499369..54502319,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10171521	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs1215147	0.81[CHD][hapmap]
rs1215149	0.88[JPT][hapmap]
rs12465259	0.81[JPT][hapmap]
rs1351881	0.88[JPT][hapmap]
rs1385274	0.82[JPT][hapmap]
rs1727506	0.83[CHD][hapmap]
rs2628196	0.99[ASN][1000 genomes]
rs6718204	0.88[JPT][hapmap]
rs6727644	0.83[JPT][hapmap]
rs843645	0.86[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap]
rs843649	0.83[JPT][hapmap]
rs843652	0.83[JPT][hapmap]
rs843655	0.94[JPT][hapmap]
rs843657	0.83[JPT][hapmap]
rs843658	0.83[CHD][hapmap]
rs843664	0.88[JPT][hapmap]
rs843694	0.83[JPT][hapmap]
rs843698	0.83[JPT][hapmap]
rs843700	0.83[JPT][hapmap]
rs843701	0.83[JPT][hapmap]
rs843704	0.89[CHD][hapmap];0.94[JPT][hapmap]
rs843707	0.83[JPT][hapmap]
rs843742	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs843755	0.88[JPT][hapmap]
rs843758	0.81[CHD][hapmap]
rs843759	0.88[JPT][hapmap]
rs860058	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv457897	chr2:54459093-54502912	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv582012	chr2:54459093-54502912	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv1004632	chr2:54469283-54590480	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv998172	chr2:54488511-54537474	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1011754	chr2:54494644-54533805	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs843743	RTN4	cis	parietal	SCAN
rs843743	CCDC104	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54481000-54502600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:54483400-54521200	Weak transcription	Pancreas	Pancrea
4	chr2:54488200-54514600	Weak transcription	Aorta	Aorta
5	chr2:54489400-54501400	Weak transcription	Fetal Muscle Leg	muscle
6	chr2:54491000-54501200	Weak transcription	HSMM	muscle
7	chr2:54495200-54503400	Weak transcription	Psoas Muscle	Psoas
8	chr2:54495400-54501400	Weak transcription	Brain Anterior Caudate	brain
9	chr2:54496000-54501600	Weak transcription	Left Ventricle	heart
10	chr2:54498400-54502400	Weak transcription	Fetal Intestine Large	intestine
11	chr2:54499200-54504000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:54499400-54502600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:54500000-54502000	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:54500200-54511800	Weak transcription	Primary B cells from cord blood	blood
15	chr2:54500200-54517800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:54500800-54501600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr2:54500800-54501600	ZNF genes & repeats	Dnd41	blood

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