Variant report

Variant	rs7918207
Chromosome Location	chr10:116187105-116187106
allele	C/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	SMC3	chr10:116187052-116187307	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr10:116187089-116187490	HepG2	liver:	n/a	n/a
3	RAD21	chr10:116186949-116187286	H1-hESC	embryonic stem cell:	n/a	chr10:116187046-116187065 chr10:116187051-116187061
4	RAD21	chr10:116186970-116187375	ECC-1	luminal epithelium:	n/a	chr10:116187046-116187065 chr10:116187051-116187061
5	RAD21	chr10:116186946-116187336	H1-hESC	embryonic stem cell:	n/a	chr10:116187046-116187065 chr10:116187051-116187061
6	TCF7L2	chr10:116186925-116187177	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr10:116186374-116190877	PANC-1	pancreas:	n/a	n/a
8	RAD21	chr10:116186900-116187293	H1-hESC	embryonic stem cell:	n/a	chr10:116187046-116187065 chr10:116187051-116187061
9	CTCF	chr10:116187060-116187357	GM12878	blood:	n/a	n/a
10	CTCF	chr10:116187010-116187285	H1-hESC	embryonic stem cell:	n/a	chr10:116187045-116187063
11	GATA3	chr10:116186902-116187154	T-47D	breast:	n/a	chr10:116187012-116187024
12	POLR2A	chr10:116186903-116187893	Hela-S3	cervix:	n/a	n/a
13	CTCF	chr10:116187080-116187230	HA-sp	spinal cord:	n/a	n/a
14	SMC3	chr10:116187054-116187240	GM12878	blood:	n/a	n/a
15	RAD21	chr10:116187021-116187317	Hela-S3	cervix:	n/a	chr10:116187046-116187065 chr10:116187051-116187061
16	CTCF	chr10:116187100-116187250	HCPEpiC	choroid plexus:	n/a	n/a
17	CTCF	chr10:116187052-116187301	A549	lung:	n/a	n/a
18	RAD21	chr10:116186906-116187500	SK-N-SH	brain:	n/a	chr10:116187046-116187065 chr10:116187420-116187434 chr10:116187051-116187061
19	POLR2A	chr10:116186743-116187572	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:116180487..116182128-chr10:116186308..116189137,2	MCF-7	breast:
2	chr10:116063583..116065131-chr10:116185778..116187439,2	MCF-7	breast:
3	chr10:116185292..116187942-chr10:116188766..116190675,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ABLIM1-2	chr10:116184204-116187157	NONHSAT016453

Variant related genes	Relation type
RN7SL384P	TF binding region
ENSG00000169129	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10787529	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10885565	0.98[ASN][1000 genomes]
rs11196731	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11196732	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11196733	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11196735	0.97[ASN][1000 genomes]
rs11196736	0.97[ASN][1000 genomes]
rs11196737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11196739	0.81[CHD][hapmap];0.83[GIH][hapmap];0.81[ASN][1000 genomes]
rs11196740	0.82[ASN][1000 genomes]
rs11551242	0.86[CHB][hapmap];0.83[CHD][hapmap];0.85[ASN][1000 genomes]
rs11817343	0.97[ASN][1000 genomes]
rs12218918	0.85[ASN][1000 genomes]
rs12219876	0.99[ASN][1000 genomes]
rs12255595	0.80[CHD][hapmap]
rs1570224	0.98[ASN][1000 genomes]
rs3750820	0.86[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs4751905	0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs4752726	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752727	0.81[ASN][1000 genomes]
rs4752728	0.81[ASN][1000 genomes]
rs58450586	0.85[ASN][1000 genomes]
rs6585278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6646	0.85[ASW][hapmap];0.82[CEU][hapmap];0.96[GIH][hapmap];0.94[LWK][hapmap];0.85[MKK][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes]
rs7075375	0.83[CHD][hapmap]
rs7081297	0.83[CHD][hapmap]
rs7090380	0.89[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7091921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7917233	0.83[CHD][hapmap]
rs7920422	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037308	chr10:116141946-116519765	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv540780	chr10:116141946-116519765	Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7918207	PNLIPRP3	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116178400-116189200	Weak transcription	Primary T cells from cord blood	blood
2	chr10:116180000-116196200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:116180800-116190200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:116181000-116189400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr10:116181000-116190400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr10:116181400-116190600	Weak transcription	HMEC	breast
7	chr10:116184400-116189400	Weak transcription	Primary B cells from peripheral blood	blood
8	chr10:116185200-116188000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr10:116185600-116187600	Enhancers	HUVEC	blood vessel
10	chr10:116185600-116188000	Enhancers	Left Ventricle	heart
11	chr10:116185800-116187600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr10:116185800-116187800	Enhancers	Adipose Nuclei	Adipose
13	chr10:116185800-116188000	Enhancers	Pancreas	Pancrea
14	chr10:116185800-116188000	Enhancers	Right Atrium	heart
15	chr10:116185800-116189800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr10:116186000-116193600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr10:116186200-116187200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr10:116186200-116187400	Weak transcription	Right Ventricle	heart
19	chr10:116186400-116187600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr10:116186400-116187800	Enhancers	Fetal Stomach	stomach
21	chr10:116186600-116187200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:116186600-116187400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr10:116186600-116187400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr10:116186600-116187400	Enhancers	Fetal Lung	lung
25	chr10:116186600-116187600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr10:116186600-116187800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:116186600-116187800	Enhancers	Fetal Muscle Trunk	muscle
28	chr10:116186600-116187800	Enhancers	Stomach Smooth Muscle	stomach
29	chr10:116186600-116188000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr10:116186600-116188000	Enhancers	Ovary	ovary
31	chr10:116186600-116193200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr10:116186600-116198200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr10:116186800-116187600	Enhancers	H1 Cell Line	embryonic stem cell
34	chr10:116186800-116187600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr10:116186800-116187600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr10:116186800-116187800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr10:116186800-116188000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr10:116186800-116188000	Enhancers	Stomach Mucosa	stomach
39	chr10:116186800-116194400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr10:116187000-116187200	Enhancers	iPS-18 Cell Line	embryonic stem cell
41	chr10:116187000-116187400	Enhancers	Fetal Muscle Leg	muscle
42	chr10:116187000-116187800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr10:116187000-116188000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr10:116187000-116210400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links