Variant report

Variant	rs9876307
Chromosome Location	chr3:194800099-194800100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194792659..194796226-chr3:194797531..194801408,5	MCF-7	breast:
2	chr3:194798845..194800970-chr3:194805695..194807508,2	K562	blood:
3	chr3:194789447..194796347-chr3:194796697..194800807,6	K562	blood:
4	chr3:194784040..194786855-chr3:194798676..194802052,3	MCF-7	breast:

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1389726	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs9861985	0.86[AFR][1000 genomes]
rs9876929	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883940	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9876307	TCF23	trans	lymphoblastoid	seeQTL
rs9876307	FLJ32063	trans	lymphoblastoid	seeQTL

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194779000-194808000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:194781000-194808000	Weak transcription	Colonic Mucosa	Colon
3	chr3:194783600-194801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:194785600-194801400	Weak transcription	Fetal Lung	lung
5	chr3:194785600-194801600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:194785600-194802000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:194786000-194800400	Weak transcription	GM12878-XiMat	blood
8	chr3:194787600-194801000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr3:194790400-194808000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr3:194790600-194800200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:194790600-194800600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:194790600-194801000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:194790600-194801600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:194790600-194801800	Weak transcription	Colon Smooth Muscle	Colon
15	chr3:194790600-194802000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:194790600-194802400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr3:194790600-194807800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:194790800-194800400	Weak transcription	Fetal Brain Female	brain
19	chr3:194790800-194800600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:194790800-194800800	Weak transcription	Esophagus	oesophagus
21	chr3:194790800-194803600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr3:194790800-194807400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:194790800-194807800	Weak transcription	HepG2	liver
24	chr3:194791000-194800400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:194791000-194801400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:194791600-194800200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:194792200-194800400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:194792400-194804200	Enhancers	Fetal Thymus	thymus
30	chr3:194793600-194801200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:194793800-194800600	Weak transcription	Primary T cells from cord blood	blood
32	chr3:194794000-194800600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:194794000-194807800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr3:194794800-194804400	Enhancers	Spleen	Spleen
35	chr3:194795400-194803800	Enhancers	Thymus	Thymus
36	chr3:194796000-194804000	Enhancers	Fetal Muscle Leg	muscle
37	chr3:194797000-194800200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:194797200-194801000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:194797200-194801600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:194797200-194808200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:194797400-194800200	Weak transcription	Primary B cells from cord blood	blood
42	chr3:194797400-194800600	Enhancers	Fetal Heart	heart
43	chr3:194797400-194802200	Weak transcription	NHLF	lung
44	chr3:194797600-194800200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:194797600-194800200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:194797800-194800800	Weak transcription	Gastric	stomach
47	chr3:194797800-194801000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr3:194797800-194801400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:194798000-194801400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:194798000-194802800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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