Variant report

Variant	rs1056104
Chromosome Location	chr2:39008949-39008950
allele	A/G
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	chr2:38993209..38995928-chr2:39007575..39009225,2	MCF-7	breast:
3	chr2:38977058..38979764-chr2:39007414..39010440,5	MCF-7	breast:
4	chr2:38978104..38979816-chr2:39008892..39011807,3	K562	blood:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12987870	0.81[TSI][hapmap]
rs13018921	0.84[AMR][1000 genomes]
rs59639671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61493373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1056104	ENSG00000152147	cis	multi-tissue	Pritchard
rs1056104	SOS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:117 , 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	chr2:39006200-39010600	Weak transcription	Stomach Mucosa	stomach
8	chr2:39006200-39025200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:39006200-39029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:39006200-39029800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr2:39006200-39031800	Weak transcription	Right Ventricle	heart
12	chr2:39006400-39009600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:39006400-39010400	Strong transcription	Fetal Intestine Small	intestine
14	chr2:39006400-39010400	Weak transcription	NH-A	brain
15	chr2:39006400-39011200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:39006400-39018800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr2:39006400-39024000	Weak transcription	Osteobl	bone
18	chr2:39006400-39025200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:39006400-39025200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:39006400-39029600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr2:39006400-39037800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:39006600-39009400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:39006600-39009400	Strong transcription	Fetal Muscle Trunk	muscle
26	chr2:39006600-39009600	Strong transcription	Fetal Thymus	thymus
27	chr2:39006600-39009800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:39006600-39009800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr2:39006600-39010200	Strong transcription	Fetal Stomach	stomach
30	chr2:39006600-39011000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr2:39006600-39011400	Weak transcription	Hela-S3	cervix
32	chr2:39006600-39025200	Weak transcription	Fetal Brain Female	brain
33	chr2:39006600-39031600	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:39006600-39032200	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:39006600-39033600	Weak transcription	GM12878-XiMat	blood
36	chr2:39006600-39038200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:39006800-39031800	Weak transcription	Fetal Brain Male	brain
38	chr2:39007000-39009000	Strong transcription	Dnd41	blood
39	chr2:39007000-39009200	Strong transcription	Fetal Muscle Leg	muscle
40	chr2:39007000-39010200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr2:39007400-39009200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:39007400-39009200	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr2:39007400-39009400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:39007400-39010200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:39007400-39012000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:39007600-39009000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:39007600-39009000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:39007600-39009000	Strong transcription	Fetal Intestine Large	intestine
49	chr2:39007600-39009000	Strong transcription	Thymus	Thymus
50	chr2:39007600-39009000	Strong transcription	Spleen	Spleen

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