Variant report

Variant	rs1260121
Chromosome Location	chr12:123246355-123246356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:123237435..123239674-chr12:123244773..123246396,2	K562	blood:
2	chr12:123235825..123239582-chr12:123243364..123250296,6	MCF-7	breast:
3	chr12:123235308..123239495-chr12:123239510..123247125,14	MCF-7	breast:
4	chr12:123245814..123248349-chr12:123249964..123253277,3	K562	blood:

Variant related genes	Relation type
ENSG00000139726	Chromatin interaction
ENSG00000206914	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1026395	1.00[JPT][hapmap]
rs1037593	1.00[JPT][hapmap]
rs10773599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]
rs10847742	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs10847749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs10847751	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10847775	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs10847910	1.00[JPT][hapmap]
rs10848148	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11059729	1.00[ASN][1000 genomes]
rs11060152	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs11060932	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11060999	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12311043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12815479	1.00[CHD][hapmap]
rs1671684	1.00[JPT][hapmap]
rs1671687	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap]
rs1696355	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1798563	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1975761	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2061099	1.00[JPT][hapmap]
rs2343107	1.00[JPT][hapmap]
rs2649894	0.87[ASN][1000 genomes]
rs2649895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649896	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649900	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2649914	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3844369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs4307760	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4759353	1.00[JPT][hapmap]
rs4759354	1.00[JPT][hapmap]
rs4759384	1.00[JPT][hapmap]
rs4759438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs548349	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6489241	1.00[CEU][hapmap]
rs651683	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7138257	1.00[JPT][hapmap]
rs7298176	1.00[JPT][hapmap]
rs7306948	1.00[JPT][hapmap]
rs7485652	1.00[JPT][hapmap]
rs7957643	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7958155	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs839354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839355	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839356	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs839357	1.00[ASN][1000 genomes]
rs839362	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs897386	0.81[CEU][hapmap]
rs897388	1.00[JPT][hapmap]
rs967281	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs9795629	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899571	chr12:123215734-123363562	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1260121	RAB35	cis	parietal	SCAN
rs1260121	KDM2B	cis	cerebellum	SCAN
rs1260121	TMEM120B	cis	parietal	SCAN
rs1260121	EIF2B1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:123238200-123249400	Weak transcription	Aorta	Aorta
2	chr12:123238400-123258000	Strong transcription	Fetal Muscle Trunk	muscle
3	chr12:123238600-123248400	Weak transcription	Right Ventricle	heart
4	chr12:123238600-123249000	Weak transcription	Fetal Heart	heart
5	chr12:123238600-123250800	Weak transcription	Stomach Mucosa	stomach
6	chr12:123238600-123255600	Strong transcription	Fetal Intestine Large	intestine
7	chr12:123238600-123255800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr12:123238600-123258800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:123238800-123246400	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:123238800-123246600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:123238800-123255600	Strong transcription	Primary B cells from peripheral blood	blood
12	chr12:123238800-123255600	Strong transcription	Fetal Muscle Leg	muscle
13	chr12:123238800-123255800	Strong transcription	Primary B cells from cord blood	blood
14	chr12:123238800-123255800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:123238800-123255800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr12:123238800-123255800	Strong transcription	Liver	Liver
17	chr12:123238800-123256000	Strong transcription	NH-A	brain
18	chr12:123238800-123256200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:123238800-123256200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr12:123238800-123256200	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:123238800-123256200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr12:123238800-123256600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:123238800-123257400	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr12:123238800-123257400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:123238800-123257600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:123238800-123257800	Strong transcription	Fetal Thymus	thymus
27	chr12:123238800-123257800	Strong transcription	Osteobl	bone
28	chr12:123238800-123258000	Strong transcription	Placenta	Placenta
29	chr12:123239000-123246400	Strong transcription	Primary T cells from cord blood	blood
30	chr12:123239000-123252600	Strong transcription	NHDF-Ad	bronchial
31	chr12:123239000-123255200	Strong transcription	Brain Hippocampus Middle	brain
32	chr12:123239000-123255600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr12:123239000-123255600	Strong transcription	Duodenum Mucosa	Duodenum
34	chr12:123239000-123255600	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr12:123239000-123256600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:123239000-123257400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr12:123239000-123257600	Strong transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:123239200-123248400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:123239200-123253000	Strong transcription	Primary hematopoietic stem cells	blood
40	chr12:123239200-123253600	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr12:123239200-123255800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:123239200-123255800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr12:123239200-123255800	Strong transcription	Adipose Nuclei	Adipose
44	chr12:123239200-123257000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr12:123239200-123257400	Strong transcription	A549	lung
46	chr12:123239200-123257800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr12:123239400-123246400	Strong transcription	Thymus	Thymus
48	chr12:123239400-123247600	Strong transcription	HMEC	breast
49	chr12:123239400-123248200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:123239400-123256800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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