Variant report

Variant	rs1548883
Chromosome Location	chr7:12279793-12279794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1020004	0.81[YRI][hapmap]
rs10215270	1.00[CEU][hapmap]
rs10251962	1.00[CEU][hapmap]
rs10256397	1.00[CEU][hapmap]
rs10259305	1.00[CEU][hapmap]
rs10268302	1.00[CEU][hapmap]
rs10270435	1.00[CEU][hapmap]
rs10271597	1.00[CEU][hapmap]
rs10273416	1.00[CEU][hapmap]
rs1079506	1.00[CEU][hapmap]
rs11971590	1.00[CEU][hapmap]
rs12699321	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs13240394	0.87[ASN][1000 genomes]
rs13244354	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1435530	0.83[ASN][1000 genomes]
rs17149894	0.85[YRI][hapmap]
rs17165694	0.83[ASN][1000 genomes]
rs17165803	0.86[ASN][1000 genomes]
rs2160268	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28459566	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28722991	0.87[ASN][1000 genomes]
rs28730406	0.87[ASN][1000 genomes]
rs5011435	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6946459	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs6972805	1.00[CEU][hapmap]
rs72582233	0.85[ASN][1000 genomes]
rs72582234	0.85[ASN][1000 genomes]
rs72582242	0.93[ASN][1000 genomes]
rs7802952	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804053	0.86[ASN][1000 genomes]
rs954660	1.00[CEU][hapmap]

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	nsv606199	chr7:11506143-12486659	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv534432	chr7:12148960-12693032	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1024554	chr7:12214722-12967418	Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv538735	chr7:12214722-12967418	Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:12252000-12280000	Weak transcription	Colonic Mucosa	Colon
2	chr7:12252000-12280000	Weak transcription	Right Ventricle	heart
3	chr7:12252000-12285400	Weak transcription	Spleen	Spleen
4	chr7:12252400-12281600	Weak transcription	HSMMtube	muscle
5	chr7:12252400-12284000	Weak transcription	Fetal Intestine Small	intestine
6	chr7:12259800-12283600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr7:12264200-12279800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr7:12264200-12280000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:12264200-12280000	Weak transcription	Ovary	ovary
10	chr7:12264600-12279800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:12266400-12279800	Weak transcription	Small Intestine	intestine
12	chr7:12270000-12284400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr7:12271800-12280000	Weak transcription	Osteobl	bone
14	chr7:12271800-12289000	Weak transcription	HSMM	muscle
15	chr7:12272400-12280000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:12274800-12280000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr7:12278000-12283800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr7:12278200-12279800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:12278200-12279800	Weak transcription	NH-A	brain
20	chr7:12278400-12280000	Weak transcription	Brain Anterior Caudate	brain
21	chr7:12278400-12280200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr7:12278400-12280200	Weak transcription	Left Ventricle	heart
23	chr7:12278400-12281000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:12278600-12279800	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr7:12278600-12280000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr7:12278600-12280200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr7:12278600-12280200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr7:12278600-12280200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:12278600-12284600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr7:12278800-12280000	Enhancers	Primary B cells from peripheral blood	blood
31	chr7:12278800-12280000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr7:12278800-12280000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr7:12278800-12280400	Weak transcription	Fetal Kidney	kidney
34	chr7:12278800-12280400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr7:12278800-12280600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr7:12278800-12280600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr7:12278800-12283600	Weak transcription	A549	lung
38	chr7:12279000-12280600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr7:12279000-12282200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr7:12279000-12284400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr7:12279200-12279800	Enhancers	Primary T cells from cord blood	blood
42	chr7:12279200-12279800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr7:12279200-12280000	Enhancers	Primary B cells from cord blood	blood
44	chr7:12279200-12280000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr7:12279200-12280000	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr7:12279200-12281000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr7:12279400-12279800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr7:12279400-12280000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
49	chr7:12279400-12281000	Weak transcription	Adipose Nuclei	Adipose
50	chr7:12279400-12281800	Weak transcription	Placenta	Placenta

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