Variant report

Variant	rs12124175
Chromosome Location	chr1:179929388-179929389
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179927273..179932264-chr1:179932290..179936939,6	K562	blood:
2	chr1:179851408..179853252-chr1:179927938..179929931,3	MCF-7	breast:
3	chr1:179921415..179925789-chr1:179925828..179929752,13	MCF-7	breast:
4	chr1:179927814..179929635-chr1:179943025..179944552,2	MCF-7	breast:
5	chr1:179890847..179892932-chr1:179926143..179929567,3	K562	blood:
6	chr1:179928179..179930214-chr1:179950625..179952274,2	MCF-7	breast:
7	chr1:179928118..179930055-chr1:179946472..179948702,2	K562	blood:

Variant related genes	Relation type
ENSG00000143337	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000272906	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10798731	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10798733	1.00[ASN][1000 genomes]
rs10913911	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913912	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913913	1.00[CHB][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913921	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913922	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];1.00[ASN][1000 genomes]
rs10913928	1.00[ASN][1000 genomes]
rs10913929	1.00[ASN][1000 genomes]
rs11579402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs11589421	1.00[CHB][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117957	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12119113	1.00[ASN][1000 genomes]
rs12120822	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs12127248	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129928	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131995	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135952	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136838	1.00[CHB][hapmap]
rs12137562	1.00[CHB][hapmap]
rs12138251	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144757	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743903	1.00[ASN][1000 genomes]
rs12744192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3845390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4083553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4652477	1.00[ASN][1000 genomes]
rs4652478	1.00[ASN][1000 genomes]
rs55676403	1.00[ASN][1000 genomes]
rs55882713	1.00[ASN][1000 genomes]
rs56166206	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58121876	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59953116	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61605706	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6425605	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6693288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6702845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72710619	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72710658	1.00[ASN][1000 genomes]
rs7521701	1.00[ASN][1000 genomes]
rs7521873	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522347	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7533903	1.00[ASN][1000 genomes]
rs7538086	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7539784	1.00[ASN][1000 genomes]
rs7550093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7555418	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9425484	1.00[CEU][hapmap]
rs9425862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9425864	1.00[ASN][1000 genomes]
rs9425869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv872573	chr1:179929388-180093066	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179924800-179935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:179924800-179937800	Weak transcription	Spleen	Spleen
3	chr1:179924800-179938000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:179924800-179938000	Weak transcription	Lung	lung
5	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:179925200-179946200	Weak transcription	Stomach Mucosa	stomach
7	chr1:179925400-179929800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:179925400-179931000	Weak transcription	Fetal Thymus	thymus
9	chr1:179925400-179946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:179925600-179930200	Weak transcription	Fetal Stomach	stomach
11	chr1:179925600-179935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:179925600-179938400	Weak transcription	HSMM	muscle
13	chr1:179925800-179929600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:179925800-179929800	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:179925800-179930200	Weak transcription	Fetal Intestine Small	intestine
16	chr1:179925800-179930600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:179925800-179933400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:179925800-179935600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:179925800-179935600	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:179925800-179937600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:179925800-179937600	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:179925800-179937600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:179925800-179937800	Weak transcription	Thymus	Thymus
24	chr1:179925800-179940600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr1:179926000-179931600	Weak transcription	Ovary	ovary
26	chr1:179926000-179937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:179926000-179938000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:179926000-179938000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:179926000-179938000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:179926000-179938000	Weak transcription	Right Atrium	heart
31	chr1:179926000-179938200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:179926000-179938400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:179926400-179930400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr1:179926400-179937800	Weak transcription	Brain Angular Gyrus	brain
35	chr1:179926600-179930800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:179926600-179933800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr1:179926800-179929400	Weak transcription	Primary T cells from cord blood	blood
38	chr1:179926800-179930800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr1:179926800-179934000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:179926800-179934200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:179926800-179934400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:179926800-179935000	Weak transcription	Primary B cells from cord blood	blood
43	chr1:179926800-179961400	Weak transcription	A549	lung
44	chr1:179927000-179930200	Weak transcription	Fetal Brain Female	brain
45	chr1:179927000-179930800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:179927000-179931000	Weak transcription	Fetal Intestine Large	intestine
47	chr1:179927000-179933400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:179927000-179933600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:179927000-179934000	Weak transcription	Osteobl	bone
50	chr1:179927000-179935600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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