Variant report

Variant	rs10487494
Chromosome Location	chr7:127220195-127220196
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:127204431..127206594-chr7:127219494..127222300,2	MCF-7	breast:
2	7:127009457-127018926..7:127216013-127221502	GM12878	blood:
3	chr7:127200505..127203389-chr7:127219797..127221382,2	K562	blood:

Variant related genes	Relation type
ENSG00000048405	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10487484	0.85[ASN][1000 genomes]
rs12536382	0.90[ASW][hapmap]
rs12536698	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs12706803	0.92[ASN][1000 genomes]
rs13227138	0.85[ASN][1000 genomes]
rs13235029	0.92[ASN][1000 genomes]
rs13244426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13247976	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13309235	0.85[ASN][1000 genomes]
rs1419408	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs17660187	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17662800	0.82[ASN][1000 genomes]
rs17730185	0.82[ASN][1000 genomes]
rs17730294	0.82[ASN][1000 genomes]
rs2272374	1.00[JPT][hapmap]
rs33973710	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34121113	0.92[ASN][1000 genomes]
rs34188289	0.82[ASN][1000 genomes]
rs34195583	0.92[ASN][1000 genomes]
rs34211107	1.00[ASN][1000 genomes]
rs34365152	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34388330	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34599926	0.96[ASN][1000 genomes]
rs34814259	0.92[ASN][1000 genomes]
rs34844752	0.82[ASN][1000 genomes]
rs34881339	0.85[ASN][1000 genomes]
rs35120956	0.82[ASN][1000 genomes]
rs35144279	0.92[ASN][1000 genomes]
rs35528098	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35640048	0.82[ASN][1000 genomes]
rs35872516	0.82[ASN][1000 genomes]
rs36046498	0.82[ASN][1000 genomes]
rs3752619	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3757785	1.00[JPT][hapmap]
rs3808111	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs3808115	1.00[JPT][hapmap]
rs58451280	0.82[ASN][1000 genomes]
rs62468943	1.00[ASN][1000 genomes]
rs62481380	0.82[ASN][1000 genomes]
rs62481384	0.82[ASN][1000 genomes]
rs62483172	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957054	0.92[ASN][1000 genomes]
rs6964793	1.00[ASN][1000 genomes]
rs746238	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7808161	0.82[ASN][1000 genomes]
rs7811506	0.96[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	nsv831122	chr7:127143207-127357885	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv971145	chr7:127215275-127220784	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10487494	LRRC4	cis	parietal	SCAN
rs10487494	HYAL4	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:127200600-127221400	Weak transcription	Pancreas	Pancrea
2	chr7:127203400-127220400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr7:127203600-127221400	Weak transcription	Left Ventricle	heart
4	chr7:127204400-127221000	Weak transcription	Aorta	Aorta
5	chr7:127208800-127221000	Weak transcription	Brain Anterior Caudate	brain
6	chr7:127209600-127221600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr7:127210200-127221600	Weak transcription	Small Intestine	intestine
8	chr7:127210400-127221000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr7:127210600-127221000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr7:127212800-127221400	Weak transcription	Spleen	Spleen
11	chr7:127213000-127221200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:127213400-127220800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr7:127213400-127221000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:127213400-127221400	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr7:127213600-127221000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr7:127214000-127220400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr7:127214600-127222000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:127214800-127221000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr7:127215000-127222000	Strong transcription	Fetal Muscle Leg	muscle
20	chr7:127215200-127221200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr7:127215200-127221200	Weak transcription	HMEC	breast
22	chr7:127215200-127221400	Weak transcription	Fetal Intestine Small	intestine
23	chr7:127215600-127220400	Weak transcription	Brain Angular Gyrus	brain
24	chr7:127215800-127220800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr7:127215800-127221200	Weak transcription	Gastric	stomach
26	chr7:127216200-127222000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:127216800-127220400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:127216800-127221200	Weak transcription	HUVEC	blood vessel
29	chr7:127216800-127222200	Weak transcription	Stomach Mucosa	stomach
30	chr7:127217000-127221200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr7:127217200-127221200	Weak transcription	Ovary	ovary
32	chr7:127217400-127220600	Strong transcription	Primary T cells from cord blood	blood
33	chr7:127217600-127221000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr7:127217600-127221400	Strong transcription	Fetal Thymus	thymus
35	chr7:127218000-127220200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr7:127218000-127220200	Strong transcription	Primary T helper cells fromperipheralblood	blood
37	chr7:127218000-127220400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr7:127218000-127221000	Strong transcription	Placenta	Placenta
39	chr7:127218000-127221600	Strong transcription	Primary B cells from peripheral blood	blood
40	chr7:127218000-127221800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr7:127218000-127222000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr7:127218000-127222000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr7:127218000-127222200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr7:127218000-127222800	Weak transcription	Hela-S3	cervix
45	chr7:127218000-127223000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr7:127218000-127223200	Strong transcription	Primary B cells from cord blood	blood
47	chr7:127218000-127223400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr7:127218000-127223400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr7:127218200-127220200	Strong transcription	GM12878-XiMat	blood
50	chr7:127218200-127220800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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