Variant report

Variant	rs10236149
Chromosome Location	chr7:98977515-98977516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:98976910..98979073-chr7:98989172..98991412,2	MCF-7	breast:
2	chr7:98975447..98980936-chr7:99003746..99008536,8	MCF-7	breast:
3	chr7:98927030..98929384-chr7:98976181..98977844,2	MCF-7	breast:
4	chr7:98975439..98979350-chr7:99003635..99008025,5	K562	blood:
5	chr7:98976344..98978332-chr7:98985918..98989033,3	MCF-7	breast:
6	chr7:98965082..98967314-chr7:98975254..98977961,2	K562	blood:
7	chr7:98976192..98977767-chr7:99011584..99014530,2	MCF-7	breast:
8	chr7:98975550..98978554-chr7:98995134..98998882,4	K562	blood:
9	chr7:98977091..98978617-chr7:99034122..99036702,2	MCF-7	breast:
10	chr17:66637981..66640873-chr7:98975754..98977781,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000106245	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000106244	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000239133	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10155966	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10243678	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10249167	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10255399	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10258757	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10267346	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10270459	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10270917	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10272998	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10274407	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10277149	0.81[EUR][1000 genomes]
rs10953287	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11762273	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11973460	0.84[AMR][1000 genomes]
rs17161698	0.86[ASN][1000 genomes]
rs2057905	0.86[ASN][1000 genomes]
rs2057906	0.87[ASN][1000 genomes]
rs2072181	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107922	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2269985	0.82[ASN][1000 genomes]
rs2286162	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2404322	0.89[ASN][1000 genomes]
rs2404323	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28495024	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28820905	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3764815	0.81[ASN][1000 genomes]
rs3801288	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6943920	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6953476	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6972337	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6975099	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9641253	0.89[AMR][1000 genomes]
rs9768020	0.86[AMR][1000 genomes];0.81[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	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10236149	ARPC1B	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:98971000-98990400	Weak transcription	Fetal Kidney	kidney
2	chr7:98973200-98978800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:98973400-98977600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr7:98973400-98977600	Weak transcription	Brain Substantia Nigra	brain
5	chr7:98973400-98977600	Weak transcription	Fetal Heart	heart
6	chr7:98973400-98977600	Weak transcription	Small Intestine	intestine
7	chr7:98973400-98978400	Weak transcription	Psoas Muscle	Psoas
8	chr7:98973400-98978600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr7:98973400-98978800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:98973400-98979000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr7:98973400-98979200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr7:98973400-98984000	Weak transcription	Aorta	Aorta
13	chr7:98973400-98984200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:98973400-98984200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:98973400-98984200	Weak transcription	Ovary	ovary
16	chr7:98973400-98984400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr7:98973400-98987400	Weak transcription	Brain Germinal Matrix	brain
18	chr7:98973400-98987800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:98973400-98989800	Weak transcription	Brain Angular Gyrus	brain
20	chr7:98974000-98977600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr7:98974200-98978200	Weak transcription	Pancreas	Pancrea
22	chr7:98974800-98979800	Strong transcription	Fetal Intestine Small	intestine
23	chr7:98975000-98978400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr7:98976000-98977600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr7:98976400-98977600	Weak transcription	Fetal Intestine Large	intestine
26	chr7:98976600-98977600	Genic enhancers	Dnd41	blood
27	chr7:98976600-98978200	Flanking Active TSS	Hela-S3	cervix
28	chr7:98976600-98978200	Enhancers	HepG2	liver
29	chr7:98976600-98978400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr7:98976600-98978600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr7:98976600-98978600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:98976600-98978600	Enhancers	NH-A	brain
33	chr7:98976600-98978800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr7:98976600-98978800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
35	chr7:98976600-98978800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr7:98976600-98979000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr7:98976600-98979200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr7:98976600-98979200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:98976600-98979200	Flanking Active TSS	GM12878-XiMat	blood
40	chr7:98976600-98979400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr7:98976800-98977600	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr7:98976800-98977600	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr7:98976800-98977600	Enhancers	Thymus	Thymus
44	chr7:98976800-98977800	Enhancers	H1 Cell Line	embryonic stem cell
45	chr7:98976800-98977800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:98976800-98977800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr7:98976800-98977800	Enhancers	Fetal Stomach	stomach
48	chr7:98976800-98977800	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr7:98976800-98977800	Transcr. at gene 5' and 3'	A549	lung
50	chr7:98976800-98977800	Enhancers	HSMM	muscle

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