Variant report

Variant	rs907060
Chromosome Location	chr3:156255087-156255088
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:156254995..156257951-chr3:156406375..156408006,2	K562	blood:
2	chr3:156254209..156257185-chr3:156353690..156355204,2	K562	blood:
3	chr3:156253286..156255939-chr3:156390314..156392368,2	K562	blood:
4	chr3:156254673..156257232-chr3:156395894..156398875,3	K562	blood:
5	chr3:156252904..156256159-chr3:156321994..156324902,3	K562	blood:
6	chr17:57915416..57917884-chr3:156253810..156255326,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction
ENSG00000243926	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1027915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513493	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs1129109	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510277	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680280	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680282	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6785996	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6797292	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs908807	0.94[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9820091	0.94[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9856073	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014755	chr3:155889430-156411894	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv829764	chr3:156174824-156347774	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
3	nsv877683	chr3:156180366-156272351	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs907060	SSR3	Cis_1M	lymphoblastoid	RTeQTL
rs907060	C3orf33	cis	cerebellum	SCAN
rs907060	KCNAB1	Cis_1M	lymphoblastoid	RTeQTL
rs907060	LXN	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156240400-156260200	Weak transcription	Esophagus	oesophagus
2	chr3:156241600-156255800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:156243000-156255200	Weak transcription	Dnd41	blood
4	chr3:156243200-156255600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:156243200-156255600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:156243200-156255800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr3:156243200-156256600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr3:156243200-156256800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:156243200-156256800	Weak transcription	GM12878-XiMat	blood
10	chr3:156243200-156257000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:156243200-156257000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:156243200-156258800	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:156243400-156256600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr3:156243400-156256800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr3:156244000-156257000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:156244600-156257000	Weak transcription	Lung	lung
17	chr3:156245000-156257000	Weak transcription	Spleen	Spleen
18	chr3:156245400-156257200	Weak transcription	Fetal Brain Male	brain
19	chr3:156246800-156263600	Weak transcription	Fetal Brain Female	brain
20	chr3:156247200-156263800	Weak transcription	Thymus	Thymus
21	chr3:156247600-156257200	Weak transcription	Hela-S3	cervix
22	chr3:156248000-156257000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:156248800-156257000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:156249000-156264600	Weak transcription	Brain Germinal Matrix	brain
25	chr3:156249800-156255400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:156250600-156257000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:156251000-156255200	Enhancers	HSMM	muscle
28	chr3:156251000-156255600	Enhancers	HSMMtube	muscle
29	chr3:156251200-156256200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:156251600-156259200	Weak transcription	Ovary	ovary
31	chr3:156252000-156255800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:156252000-156257000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:156252000-156257000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:156252000-156257000	Weak transcription	Primary T cells from cord blood	blood
35	chr3:156252000-156263200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr3:156252000-156270200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:156252200-156255600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:156252200-156257000	Weak transcription	Aorta	Aorta
39	chr3:156252200-156268600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr3:156252400-156255400	Enhancers	NHDF-Ad	bronchial
41	chr3:156252400-156255600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr3:156252600-156256600	Weak transcription	Fetal Lung	lung
43	chr3:156253000-156256800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:156253000-156259200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:156253400-156256800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:156253400-156256800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:156253400-156257000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr3:156253400-156257400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr3:156253400-156260800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:156253400-156268200	Weak transcription	Gastric	stomach

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