Variant report

Variant	rs12024850
Chromosome Location	chr1:197887980-197887981
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:197744558..197746158-chr1:197886522..197888177,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213047	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10922333	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10922334	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11577674	0.85[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12046958	0.85[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12727777	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12729300	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12750987	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1909507	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2358777	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34100116	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3894699	0.89[YRI][hapmap]
rs4147202	0.92[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999662	chr1:197821769-197892803	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
2	esv2762214	chr1:197821769-197897496	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12024850	B3GALT2	cis	parietal	SCAN
rs12024850	KCNT2	cis	cerebellum	SCAN
rs12024850	DENND1B	cis	parietal	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197884600-197891000	Bivalent Enhancer	Fetal Thymus	thymus
2	chr1:197885000-197889000	Active TSS	Ovary	ovary
3	chr1:197885600-197888000	Bivalent Enhancer	Placenta	Placenta
4	chr1:197885800-197888400	Bivalent Enhancer	Fetal Heart	heart
5	chr1:197886000-197888600	Bivalent/Poised TSS	Osteobl	bone
6	chr1:197886200-197888600	Bivalent/Poised TSS	Brain Anterior Caudate	brain
7	chr1:197886600-197888400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
8	chr1:197886800-197888200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
9	chr1:197887000-197889400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:197887200-197889000	Active TSS	Right Atrium	heart
11	chr1:197887400-197888000	Bivalent Enhancer	Stomach Mucosa	stomach
12	chr1:197887400-197888200	Bivalent Enhancer	Fetal Intestine Large	intestine
13	chr1:197887400-197888400	Bivalent Enhancer	Fetal Stomach	stomach
14	chr1:197887400-197888800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr1:197887400-197890400	Bivalent Enhancer	Fetal Intestine Small	intestine
16	chr1:197887400-197890600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
17	chr1:197887400-197890800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:197887600-197888000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:197887600-197888000	Bivalent Enhancer	Liver	Liver
20	chr1:197887600-197888200	Bivalent/Poised TSS	Brain Substantia Nigra	brain
21	chr1:197887600-197888400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
22	chr1:197887600-197888400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:197887600-197888600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr1:197887600-197888800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:197887600-197888800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
26	chr1:197887600-197889000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
27	chr1:197887600-197889000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
28	chr1:197887600-197889000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:197887600-197889000	Bivalent Enhancer	Brain Hippocampus Middle	brain
30	chr1:197887600-197889600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:197887600-197890800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:197887800-197888000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr1:197887800-197888000	Bivalent Enhancer	Primary B cells from cord blood	blood
34	chr1:197887800-197888000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
35	chr1:197887800-197888000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
36	chr1:197887800-197888000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:197887800-197888000	Bivalent Enhancer	Duodenum Mucosa	Duodenum
38	chr1:197887800-197888000	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr1:197887800-197888000	Bivalent Enhancer	Psoas Muscle	Psoas
40	chr1:197887800-197888200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr1:197887800-197888200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
42	chr1:197887800-197888200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:197887800-197888200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
44	chr1:197887800-197888200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
45	chr1:197887800-197888200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:197887800-197888200	Enhancers	Pancreas	Pancrea
47	chr1:197887800-197888400	Bivalent Enhancer	Colonic Mucosa	Colon
48	chr1:197887800-197888400	Enhancers	Right Ventricle	heart
49	chr1:197887800-197888400	Bivalent Enhancer	NHEK	skin
50	chr1:197887800-197888600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood

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