Variant report

Variant	rs10250902
Chromosome Location	chr7:16642676-16642677
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:16641415..16643036-chr7:16685793..16687476,2	MCF-7	breast:
2	chr7:16637135..16639582-chr7:16641679..16644005,2	K562	blood:
3	chr7:16642489..16644865-chr7:16673141..16675282,2	K562	blood:

Variant related genes	Relation type
ENSG00000136261	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10247772	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10273896	0.88[EUR][1000 genomes]
rs10274133	0.88[EUR][1000 genomes]
rs10282627	0.82[ASN][1000 genomes]
rs1044984	0.84[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11765150	0.88[JPT][hapmap]
rs11772957	0.82[ASN][1000 genomes]
rs13228317	0.93[ASN][1000 genomes]
rs13244745	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2240434	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2286230	0.84[ASN][1000 genomes]
rs28498382	0.85[ASN][1000 genomes]
rs6973195	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6973197	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7156	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7796550	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7796676	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7802116	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016642	chr7:15884061-16799788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer 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
2	nsv1028125	chr7:16529160-16847225	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv830912	chr7:16623196-16791974	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv887758	chr7:16632561-16668034	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1024059	chr7:16639432-16836425	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv522819	chr7:16639615-16655387	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:16624000-16645600	Weak transcription	Gastric	stomach
2	chr7:16627800-16654200	Weak transcription	Brain Angular Gyrus	brain
3	chr7:16630400-16643000	Weak transcription	HUVEC	blood vessel
4	chr7:16630800-16643000	Weak transcription	Thymus	Thymus
5	chr7:16632600-16643200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr7:16634200-16649600	Weak transcription	Hela-S3	cervix
7	chr7:16635600-16654800	Weak transcription	Spleen	Spleen
8	chr7:16636200-16649400	Weak transcription	Small Intestine	intestine
9	chr7:16636400-16682600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:16636600-16642800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr7:16636600-16648800	Weak transcription	HMEC	breast
12	chr7:16637200-16643200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr7:16637400-16668400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr7:16637600-16644800	Strong transcription	Dnd41	blood
15	chr7:16637600-16644800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr7:16637800-16644600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr7:16637800-16644600	Strong transcription	Primary T cells from cord blood	blood
18	chr7:16637800-16644600	Strong transcription	Liver	Liver
19	chr7:16637800-16644600	Strong transcription	HSMM	muscle
20	chr7:16637800-16644800	Strong transcription	Adipose Nuclei	Adipose
21	chr7:16637800-16644800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr7:16637800-16644800	Strong transcription	Stomach Smooth Muscle	stomach
23	chr7:16637800-16649800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr7:16637800-16651600	Strong transcription	Fetal Muscle Leg	muscle
25	chr7:16637800-16652000	Strong transcription	Fetal Muscle Trunk	muscle
26	chr7:16637800-16654800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:16637800-16661600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr7:16637800-16664800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr7:16638000-16642800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr7:16638000-16644000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr7:16638000-16644800	Strong transcription	Placenta	Placenta
32	chr7:16638000-16649000	Strong transcription	Fetal Stomach	stomach
33	chr7:16638000-16656200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr7:16638000-16658800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:16638000-16660200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr7:16638000-16670800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:16638200-16655200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:16638200-16656200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr7:16638200-16659800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr7:16638400-16643200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:16638400-16647200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr7:16638400-16654800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr7:16638400-16661600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr7:16638400-16670000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr7:16638400-16670200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr7:16638800-16644800	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr7:16639000-16644000	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr7:16639000-16644200	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr7:16639000-16644600	Strong transcription	Ovary	ovary
50	chr7:16639000-16646400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links