Variant report

Variant	rs7859873
Chromosome Location	chr9:79268693-79268694
allele	C/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	TCF12	chr9:79268686-79270613	SK-N-SH	brain:	n/a	chr9:79269822-79269830
2	JUND	chr9:79268171-79270881	SK-N-SH	brain:	n/a	chr9:79270312-79270321 chr9:79269865-79269874 chr9:79270618-79270627

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79073774..79075631-chr9:79267070..79269675,2	MCF-7	breast:

Variant related genes	Relation type
PRUNE2	TF binding region
ENSG00000187210	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10521475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11144986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11144987	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11144992	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11144996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17062768	1.00[CEU][hapmap]
rs17062772	1.00[CEU][hapmap]
rs17062775	1.00[CEU][hapmap]
rs17062778	1.00[CEU][hapmap]
rs17062858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1854441	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1952460	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2067501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs499746	1.00[CEU][hapmap]
rs57389265	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs634063	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs637207	1.00[CEU][hapmap]
rs644893	1.00[CEU][hapmap]
rs7027074	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7028756	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7038619	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7039310	1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.96[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7045505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7847922	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv893479	chr9:78971253-79275226	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv949417	chr9:79078703-79282589	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79252600-79278000	Weak transcription	Gastric	stomach
2	chr9:79258000-79270000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:79259000-79269200	Weak transcription	Brain Substantia Nigra	brain
4	chr9:79259000-79278000	Weak transcription	Spleen	Spleen
5	chr9:79260000-79282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:79263600-79272800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:79263600-79282200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:79265400-79269200	Genic enhancers	HSMM	muscle
9	chr9:79265400-79270800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:79265600-79269600	Weak transcription	Brain Angular Gyrus	brain
11	chr9:79265600-79270600	Enhancers	Fetal Thymus	thymus
12	chr9:79265600-79270600	Enhancers	NHLF	lung
13	chr9:79265600-79274000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:79265800-79268800	Weak transcription	Fetal Heart	heart
15	chr9:79266000-79268800	Weak transcription	Stomach Mucosa	stomach
16	chr9:79266000-79278000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr9:79266400-79268800	Weak transcription	Fetal Muscle Leg	muscle
18	chr9:79266400-79269200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr9:79266400-79269800	Weak transcription	Brain Hippocampus Middle	brain
20	chr9:79266400-79269800	Enhancers	Osteobl	bone
21	chr9:79266400-79271400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr9:79266400-79272000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
24	chr9:79266600-79269800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr9:79266600-79270400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr9:79266600-79274200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr9:79266600-79282200	Weak transcription	Brain Anterior Caudate	brain
28	chr9:79266800-79269000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:79266800-79269400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr9:79266800-79269600	Enhancers	Primary B cells from cord blood	blood
31	chr9:79266800-79269800	Enhancers	HUVEC	blood vessel
32	chr9:79266800-79272600	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:79267000-79269000	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr9:79267000-79269200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr9:79267000-79269600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr9:79267000-79269800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr9:79267000-79270000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr9:79267000-79271400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr9:79267000-79271600	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:79267000-79271800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr9:79267000-79273200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr9:79267200-79268800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:79267200-79269000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr9:79267200-79269000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr9:79267200-79269000	Enhancers	HSMMtube	muscle
46	chr9:79267200-79269200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:79267200-79269600	Weak transcription	Primary T cells from cord blood	blood
48	chr9:79267200-79269800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:79267200-79273400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr9:79267400-79268800	Weak transcription	Fetal Intestine Small	intestine

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