Variant report

Variant	rs28177
Chromosome Location	chr7:8016899-8016900
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:8016185-8017754	GM12878	blood:	n/a	n/a
2	CUX1	chr7:8016730-8016929	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:8016755..8018272-chr7:8032373..8035088,2	K562	blood:
2	chr7:8016682..8018691-chr7:8023208..8025599,2	MCF-7	breast:
3	chr7:8016338..8018811-chr7:8026553..8029436,2	MCF-7	breast:
4	chr7:8006834..8014864-chr7:8015250..8023851,23	K562	blood:

Variant related genes	Relation type
ENSG00000233264	TF binding region
ENSG00000106415	Chromatin interaction
ENSG00000233108	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10253260	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs10257285	0.88[CEU][hapmap]
rs10265283	0.88[CEU][hapmap]
rs10272512	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2159510	0.90[YRI][hapmap];0.83[AMR][1000 genomes]
rs258851	0.91[YRI][hapmap]
rs35953256	0.83[AMR][1000 genomes]
rs37968	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs37984	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs37985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs37990	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs37991	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38005	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4725058	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4725063	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4725066	0.83[CEU][hapmap];0.80[AMR][1000 genomes]
rs4725069	0.88[CEU][hapmap]
rs6463754	0.83[AMR][1000 genomes]
rs6463755	0.88[CEU][hapmap];0.83[AMR][1000 genomes]
rs6463759	0.81[CEU][hapmap]
rs6943211	0.82[EUR][1000 genomes]
rs6974264	0.88[CEU][hapmap]
rs6975078	0.92[CEU][hapmap];0.82[AMR][1000 genomes]
rs6975913	0.81[AMR][1000 genomes]
rs7795506	0.84[CEU][hapmap]
rs7798367	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7806440	0.85[AMR][1000 genomes]
rs929509	0.91[CEU][hapmap];0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2752177	chr7:7729247-8177689	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv917172	chr7:7854632-8807385	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv1030180	chr7:7860424-8059221	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv3346837	chr7:7915187-8068557	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1020161	chr7:7929384-8047553	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28177	GLCCI1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:8010800-8023600	Weak transcription	Psoas Muscle	Psoas
2	chr7:8011400-8023600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr7:8012000-8017400	Weak transcription	Placenta	Placenta
4	chr7:8012000-8017400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr7:8012000-8017400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr7:8012000-8017600	Weak transcription	Aorta	Aorta
7	chr7:8012000-8018600	Weak transcription	Adipose Nuclei	Adipose
8	chr7:8012000-8018800	Weak transcription	Fetal Lung	lung
9	chr7:8012000-8020000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:8012200-8017000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:8012200-8017400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr7:8012200-8017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr7:8012200-8018000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr7:8012200-8018000	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr7:8012200-8018400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:8012200-8020600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr7:8012400-8018200	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr7:8012800-8017000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:8012800-8017200	Weak transcription	K562	blood
20	chr7:8012800-8017400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:8012800-8019200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr7:8012800-8019600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:8012800-8021000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr7:8013000-8017000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr7:8013000-8017600	Weak transcription	Liver	Liver
26	chr7:8013200-8018000	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr7:8013400-8017000	Weak transcription	Fetal Heart	heart
28	chr7:8013400-8017400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:8013400-8017400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr7:8013400-8018000	Enhancers	Dnd41	blood
31	chr7:8013400-8029000	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:8013400-8029600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr7:8014000-8018000	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr7:8014000-8019600	Enhancers	Primary T cells from cord blood	blood
35	chr7:8014200-8028600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:8014600-8017600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr7:8014800-8017800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr7:8015000-8017400	Weak transcription	Brain Angular Gyrus	brain
39	chr7:8015000-8045000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr7:8015200-8017600	Weak transcription	Brain Anterior Caudate	brain
41	chr7:8015200-8031800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:8015600-8017200	Enhancers	Primary B cells from peripheral blood	blood
43	chr7:8015600-8017800	Enhancers	Hela-S3	cervix
44	chr7:8015800-8017000	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr7:8015800-8017000	Weak transcription	Brain Germinal Matrix	brain
46	chr7:8015800-8023200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr7:8016200-8017400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
48	chr7:8016200-8017800	Enhancers	Primary B cells from cord blood	blood
49	chr7:8016400-8017000	Enhancers	Primary hematopoietic stem cells	blood
50	chr7:8016400-8017000	Weak transcription	Fetal Stomach	stomach

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