Variant report

Variant	rs12140137
Chromosome Location	chr1:224374882-224374883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:224369367..224372466-chr1:224374660..224377497,3	MCF-7	breast:
2	chr1:224368636..224372565-chr1:224373050..224376148,4	MCF-7	breast:
3	chr1:224374669..224377400-chr1:224391823..224393961,2	K562	blood:

Variant related genes	Relation type
ENSG00000143753	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10799491	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10799507	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10799543	0.92[EUR][1000 genomes]
rs10916414	0.91[AMR][1000 genomes]
rs10916458	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916462	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10916472	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10916481	0.85[EUR][1000 genomes]
rs10916497	0.92[EUR][1000 genomes]
rs10916498	0.89[EUR][1000 genomes]
rs12082619	0.92[EUR][1000 genomes]
rs12083770	0.96[EUR][1000 genomes]
rs12120308	0.96[EUR][1000 genomes]
rs12124547	0.92[EUR][1000 genomes]
rs12126765	0.87[EUR][1000 genomes]
rs12126815	0.84[EUR][1000 genomes]
rs12133599	0.96[EUR][1000 genomes]
rs12138866	0.92[EUR][1000 genomes]
rs12184283	0.92[EUR][1000 genomes]
rs45583539	0.92[EUR][1000 genomes]
rs60256604	0.88[EUR][1000 genomes]
rs6660194	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6686449	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6701036	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68073536	0.89[EUR][1000 genomes]
rs72751651	0.83[EUR][1000 genomes]
rs72753956	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72753969	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72753980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72753994	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72754000	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72754001	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72755905	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514140	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7552239	0.92[EUR][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	nsv832692	chr1:224206536-224407717	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv8857	chr1:224359943-224383023	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv873223	chr1:224367232-224467117	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224372200-224375000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:224372200-224377200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr1:224372200-224377400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
4	chr1:224372200-224377400	Weak transcription	Fetal Intestine Large	intestine
5	chr1:224372400-224375800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
6	chr1:224372400-224377400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:224372400-224379600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:224372400-224380200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:224372400-224381000	Weak transcription	HSMMtube	muscle
10	chr1:224372400-224389200	Weak transcription	Fetal Kidney	kidney
11	chr1:224372600-224375000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:224372600-224375200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:224372600-224375200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:224372600-224375400	Enhancers	Left Ventricle	heart
15	chr1:224372600-224377400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr1:224372600-224377400	Weak transcription	NH-A	brain
17	chr1:224372600-224379000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:224372600-224379600	Weak transcription	HMEC	breast
19	chr1:224372600-224380000	Weak transcription	Thymus	Thymus
20	chr1:224372600-224391000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:224372600-224392400	Weak transcription	Ovary	ovary
22	chr1:224372600-224392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:224372800-224376000	Strong transcription	Fetal Intestine Small	intestine
24	chr1:224372800-224380000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:224372800-224380000	Weak transcription	HSMM	muscle
26	chr1:224372800-224381000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:224372800-224392000	Weak transcription	Colon Smooth Muscle	Colon
28	chr1:224373000-224383600	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr1:224373200-224375200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr1:224373200-224375800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:224373200-224376000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:224373200-224376000	Strong transcription	Fetal Stomach	stomach
33	chr1:224373200-224376000	Strong transcription	Osteobl	bone
34	chr1:224373200-224377000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr1:224373200-224377200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:224373200-224377400	Weak transcription	Primary T cells from cord blood	blood
37	chr1:224373200-224377400	Weak transcription	Primary hematopoietic stem cells	blood
38	chr1:224373200-224377600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:224373200-224380200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:224373200-224380200	Weak transcription	HUVEC	blood vessel
41	chr1:224373200-224380400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr1:224373200-224382000	Weak transcription	Brain Substantia Nigra	brain
43	chr1:224373200-224392400	Weak transcription	Colonic Mucosa	Colon
44	chr1:224373400-224375600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr1:224373400-224376000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:224373400-224378200	Strong transcription	A549	lung
47	chr1:224373400-224379600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:224373400-224379600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:224373400-224381200	Weak transcription	Aorta	Aorta
50	chr1:224373400-224383600	Weak transcription	Small Intestine	intestine

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