Variant report

Variant	rs4907254
Chromosome Location	chr2:97549668-97549669
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97547842..97556078-chr2:97610100..97619985,30	MCF-7	breast:
2	chr2:97548252..97550212-chr2:97588588..97591450,2	MCF-7	breast:
3	chr2:97548965..97553137-chr2:97593651..97595519,4	MCF-7	breast:
4	chr2:97548625..97551257-chr21:9825962..9828708,2	MCF-7	breast:
5	chr2:97548465..97553435-chr2:97558286..97563042,6	K562	blood:
6	chr2:97549380..97552349-chr2:97593261..97597032,3	K562	blood:
7	chr2:97548880..97549708-chr2:97568977..97569712,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168754	Chromatin interaction
ENSG00000264063	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11902657	0.83[AFR][1000 genomes]
rs12464868	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12473528	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13430237	1.00[ASW][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2314652	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2314653	0.94[ASW][hapmap];0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.80[LWK][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4243786	1.00[ASW][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes]
rs6750988	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72942920	0.81[AFR][1000 genomes]
rs7581764	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs7583821	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
7	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
8	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	nsv874681	chr2:97410949-97577343	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
10	nsv874682	chr2:97423626-97567389	Transcr. at gene 5' and 3' Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4907254	TXNDC9	cis	cerebellum	SCAN
rs4907254	NEURL3	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97536800-97551800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr2:97536800-97555200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:97540200-97549800	Weak transcription	Liver	Liver
4	chr2:97540800-97552200	Weak transcription	Colon Smooth Muscle	Colon
5	chr2:97542200-97553000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:97542800-97557400	Enhancers	Placenta	Placenta
7	chr2:97544600-97550800	Weak transcription	Brain Angular Gyrus	brain
8	chr2:97544600-97550800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:97544600-97551800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:97544800-97549800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:97544800-97550800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:97545000-97550000	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:97545600-97550000	Enhancers	Fetal Thymus	thymus
14	chr2:97545600-97551400	Weak transcription	Fetal Brain Male	brain
15	chr2:97545800-97554200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr2:97546000-97555000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr2:97546600-97552400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr2:97546800-97551000	Enhancers	Left Ventricle	heart
19	chr2:97547200-97550000	Weak transcription	Stomach Mucosa	stomach
20	chr2:97547200-97550400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:97547400-97550800	Weak transcription	Brain Anterior Caudate	brain
22	chr2:97547400-97550800	Enhancers	Stomach Smooth Muscle	stomach
23	chr2:97547400-97553200	Weak transcription	Fetal Brain Female	brain
24	chr2:97547400-97553400	Weak transcription	GM12878-XiMat	blood
25	chr2:97547600-97553200	Weak transcription	Brain Germinal Matrix	brain
26	chr2:97547800-97550600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:97547800-97550600	Enhancers	HMEC	breast
28	chr2:97547800-97555000	Enhancers	Esophagus	oesophagus
29	chr2:97548000-97550600	Weak transcription	Fetal Lung	lung
30	chr2:97548200-97550000	Weak transcription	Lung	lung
31	chr2:97548200-97553200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:97548200-97553200	Weak transcription	Pancreas	Pancrea
33	chr2:97548200-97555400	Enhancers	Fetal Muscle Leg	muscle
34	chr2:97548400-97549800	Enhancers	K562	blood
35	chr2:97548400-97550200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:97548400-97550800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:97548400-97552000	Weak transcription	Right Atrium	heart
38	chr2:97548400-97553000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr2:97548400-97553200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr2:97548400-97553200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:97548600-97550600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr2:97548600-97550600	Enhancers	NHEK	skin
43	chr2:97548600-97551800	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:97548600-97556000	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr2:97548800-97552400	Weak transcription	HSMMtube	muscle
46	chr2:97548800-97553400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:97549000-97551000	Enhancers	Adipose Nuclei	Adipose
48	chr2:97549000-97552000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:97549000-97553000	Weak transcription	HSMM	muscle
50	chr2:97549000-97553200	Enhancers	Spleen	Spleen

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