Variant report

Variant	rs10912860
Chromosome Location	chr1:174941532-174941533
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:174941301-174941577	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr1:174940817-174941873	MCF-7	breast:	n/a	chr1:174941681-174941697
3	GATA3	chr1:174941133-174941731	MCF-7	breast:	n/a	chr1:174941681-174941697

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:174940560..174943499-chr1:174966339..174968094,3	K562	blood:
2	chr1:174936174..174937775-chr1:174941004..174942610,2	MCF-7	breast:
3	chr1:174940526..174942597-chr1:174943859..174946428,2	K562	blood:
4	chr1:174940853..174943825-chr1:174966754..174969423,2	MCF-7	breast:
5	chr1:174939098..174941697-chr1:174958676..174960962,2	K562	blood:
6	chr1:174938092..174940324-chr1:174940877..174942790,2	MCF-7	breast:
7	chr1:174941236..174943096-chr1:174956615..174959571,2	MCF-7	breast:
8	chr1:174927580..174945830-chr1:174955726..174971213,32	K562	blood:

No data

Variant related genes	Relation type
RABGAP1L	TF binding region
ENSG00000152061	Chromatin interaction
ENSG00000252552	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10912867	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11582831	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12119351	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12122361	1.00[CHB][hapmap]
rs12122399	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12124150	0.92[EUR][1000 genomes]
rs12125682	0.92[EUR][1000 genomes]
rs12723394	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12753457	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34484492	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56978149	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59663317	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6691857	1.00[CHB][hapmap]
rs6700816	1.00[CHB][hapmap]
rs7537508	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7550448	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10912860	RC3H1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174910800-174957000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:174924200-174967800	Weak transcription	Brain Germinal Matrix	brain
3	chr1:174924400-174958200	Weak transcription	Fetal Brain Male	brain
4	chr1:174932600-174941600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:174933000-174953600	Weak transcription	Fetal Heart	heart
6	chr1:174934600-174943800	Weak transcription	Pancreas	Pancrea
7	chr1:174934800-174943800	Weak transcription	Aorta	Aorta
8	chr1:174935000-174942200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:174935000-174943800	Weak transcription	Lung	lung
10	chr1:174935000-174959000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:174935000-174964000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr1:174935000-174967000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:174935200-174943400	Weak transcription	Brain Angular Gyrus	brain
14	chr1:174935200-174943400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr1:174935200-174943800	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:174935200-174959000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr1:174935200-174959600	Weak transcription	Esophagus	oesophagus
18	chr1:174935400-174943600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:174935400-174958400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr1:174935600-174943800	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:174935800-174959600	Weak transcription	Fetal Kidney	kidney
22	chr1:174936000-174943800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr1:174936000-174944600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:174936000-174945000	Weak transcription	NHEK	skin
25	chr1:174936000-174946200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:174936000-174950600	Weak transcription	Fetal Brain Female	brain
27	chr1:174936000-174958600	Weak transcription	Brain Substantia Nigra	brain
28	chr1:174936600-174943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:174936600-174945400	Weak transcription	Fetal Lung	lung
30	chr1:174937000-174943800	Weak transcription	Ovary	ovary
31	chr1:174937000-174963600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:174937200-174955000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:174937400-174944200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:174937400-174963600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:174937800-174942200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr1:174938000-174963600	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:174938400-174943800	Weak transcription	Spleen	Spleen
38	chr1:174938400-174945600	Weak transcription	A549	lung
39	chr1:174938600-174942400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:174938600-174943400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr1:174938600-174943400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:174938600-174945200	Weak transcription	Adipose Nuclei	Adipose
43	chr1:174938600-174952000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr1:174938600-174959000	Weak transcription	Small Intestine	intestine
45	chr1:174938600-174959400	Weak transcription	Psoas Muscle	Psoas
46	chr1:174938600-174965200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:174938800-174941600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:174938800-174943400	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr1:174938800-174951600	Weak transcription	Left Ventricle	heart
50	chr1:174938800-174959000	Weak transcription	Thymus	Thymus

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