Variant report

Variant	rs6712917
Chromosome Location	chr2:39011748-39011749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
2	chr2:39009539..39012325-chr2:39014609..39017212,2	K562	blood:
3	chr2:39003810..39007416-chr2:39010391..39012496,4	MCF-7	breast:
4	chr2:39010149..39012211-chr2:39018515..39021325,3	MCF-7	breast:
5	chr2:38976960..38980095-chr2:39010307..39015604,4	K562	blood:
6	chr2:38978104..38979816-chr2:39008892..39011807,3	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1376461	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17023025	0.82[JPT][hapmap]
rs3099947	1.00[JPT][hapmap]
rs3099967	0.84[ASN][1000 genomes]
rs3112138	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3112158	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3112160	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3112164	1.00[JPT][hapmap]
rs3112176	0.84[JPT][hapmap]
rs3112213	0.84[ASN][1000 genomes]
rs59473852	1.00[ASN][1000 genomes]
rs6544182	1.00[JPT][hapmap]
rs6707855	0.84[ASN][1000 genomes]
rs6722478	1.00[JPT][hapmap]
rs6748000	1.00[JPT][hapmap]
rs6760524	0.85[JPT][hapmap]
rs6761115	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7368897	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs921433	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription 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 target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
4	nsv1014616	chr2:38985472-39022893	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6712917	SOS1	cis	multi-tissue	Pritchard

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39005800-39037400	Weak transcription	Esophagus	oesophagus
2	chr2:39006000-39011800	Weak transcription	Pancreas	Pancrea
3	chr2:39006000-39012400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:39006000-39016000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
6	chr2:39006000-39037600	Weak transcription	Gastric	stomach
7	chr2:39006200-39025200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr2:39006200-39029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:39006200-39029800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:39006200-39031800	Weak transcription	Right Ventricle	heart
11	chr2:39006400-39018800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:39006400-39024000	Weak transcription	Osteobl	bone
13	chr2:39006400-39025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:39006400-39025200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr2:39006400-39029600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:39006400-39037800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:39006600-39025200	Weak transcription	Fetal Brain Female	brain
20	chr2:39006600-39031600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:39006600-39032200	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:39006600-39033600	Weak transcription	GM12878-XiMat	blood
23	chr2:39006600-39038200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:39006800-39031800	Weak transcription	Fetal Brain Male	brain
25	chr2:39007400-39012000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:39008800-39024200	Weak transcription	Left Ventricle	heart
27	chr2:39009000-39011800	Weak transcription	Brain Germinal Matrix	brain
28	chr2:39009000-39024600	Weak transcription	Spleen	Spleen
29	chr2:39009000-39024600	Weak transcription	Dnd41	blood
30	chr2:39009000-39027400	Weak transcription	Thymus	Thymus
31	chr2:39009000-39027800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:39009000-39029200	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr2:39009000-39037400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr2:39009200-39011800	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:39009200-39011800	Weak transcription	HSMMtube	muscle
36	chr2:39009200-39012800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr2:39009200-39015400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr2:39009200-39018600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr2:39009200-39018600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr2:39009200-39024000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr2:39009200-39024200	Weak transcription	Brain Anterior Caudate	brain
42	chr2:39009200-39024400	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:39009200-39024400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:39009200-39024400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:39009200-39024600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:39009200-39024600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr2:39009200-39024600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:39009200-39025000	Weak transcription	HSMM	muscle
49	chr2:39009200-39027600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr2:39009200-39027800	Weak transcription	Brain Substantia Nigra	brain

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