Variant report

Variant	rs13383541
Chromosome Location	chr2:39031979-39031980
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38976392..38979029-chr2:39027754..39033871,6	K562	blood:
2	chr2:39013355..39015895-chr2:39031959..39033767,2	K562	blood:
3	chr2:39027550..39029197-chr2:39030852..39032406,2	K562	blood:
4	chr2:38976891..38979056-chr2:39028521..39033921,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10168789	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10173118	0.89[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10173240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10176932	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs10197412	0.84[CEU][hapmap]
rs10779923	0.86[JPT][hapmap]
rs10865143	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10865144	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11124646	0.88[CHB][hapmap]
rs11694383	0.94[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11889280	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12465043	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12468732	0.88[ASN][1000 genomes]
rs12469681	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12473036	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12477252	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12618118	0.83[EUR][1000 genomes]
rs12623330	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs12712621	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712622	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12712624	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12712625	0.81[JPT][hapmap]
rs12712627	0.81[JPT][hapmap]
rs12991609	0.81[EUR][1000 genomes]
rs12996194	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13011522	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13014136	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13029406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13411868	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13417196	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1530852	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530853	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1979142	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1997377	0.81[CHB][hapmap]
rs2037875	0.84[CEU][hapmap]
rs2272445	0.88[CHB][hapmap]
rs3099940	0.81[CHB][hapmap]
rs3099952	0.82[ASN][1000 genomes]
rs3099965	0.94[EUR][1000 genomes]
rs3099984	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3099985	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3099987	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3099988	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099989	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3099991	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112140	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3112149	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3112198	0.88[EUR][1000 genomes]
rs3112200	0.89[CEU][hapmap];0.94[CHB][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112205	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3112209	0.81[ASN][1000 genomes]
rs3112210	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3112215	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs3112216	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs373300	0.86[JPT][hapmap]
rs3770681	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4265996	0.87[JPT][hapmap]
rs4602206	0.89[CEU][hapmap];0.94[CHB][hapmap];0.82[EUR][1000 genomes]
rs4630748	0.88[CEU][hapmap];0.88[CHB][hapmap];0.81[EUR][1000 genomes]
rs4670894	0.91[ASN][1000 genomes]
rs4670896	0.81[AFR][1000 genomes]
rs4670897	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56393601	0.82[AFR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60012208	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62144837	0.88[EUR][1000 genomes]
rs6715866	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6723868	0.95[ASN][1000 genomes]
rs6728394	0.88[CHB][hapmap]
rs6746818	0.89[CEU][hapmap]
rs6753251	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6756847	0.88[CHB][hapmap]
rs7419616	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7419838	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7565111	0.86[JPT][hapmap]
rs7588621	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7589162	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7591959	0.85[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7598922	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs7602287	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7603676	0.88[CHB][hapmap]

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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13383541	SFRS7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39005800-39037400	Weak transcription	Esophagus	oesophagus
2	chr2:39006000-39037600	Weak transcription	Aorta	Aorta
3	chr2:39006000-39037600	Weak transcription	Gastric	stomach
4	chr2:39006400-39037800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr2:39006400-39045600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:39006400-39085600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:39006600-39032200	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:39006600-39033600	Weak transcription	GM12878-XiMat	blood
9	chr2:39006600-39038200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:39009000-39037400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:39009200-39032000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:39009200-39032000	Weak transcription	K562	blood
13	chr2:39009200-39032400	Weak transcription	Primary B cells from cord blood	blood
14	chr2:39009200-39032400	Weak transcription	Brain Angular Gyrus	brain
15	chr2:39009200-39037600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:39009200-39037600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:39009200-39037600	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:39009200-39037600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:39009200-39037600	Weak transcription	NHDF-Ad	bronchial
20	chr2:39009200-39037800	Weak transcription	NHEK	skin
21	chr2:39009200-39042600	Weak transcription	Fetal Kidney	kidney
22	chr2:39009200-39050000	Weak transcription	HMEC	breast
23	chr2:39009200-39052800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr2:39009400-39037600	Weak transcription	NHLF	lung
25	chr2:39009600-39037600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:39009600-39037600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr2:39012000-39037600	Weak transcription	Pancreas	Pancrea
28	chr2:39012200-39037600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:39017600-39042200	Weak transcription	Small Intestine	intestine
30	chr2:39018400-39037600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:39019000-39057800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:39021400-39038000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:39021600-39038000	Weak transcription	Colonic Mucosa	Colon
34	chr2:39022000-39042600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:39022000-39066800	Weak transcription	Stomach Mucosa	stomach
36	chr2:39022400-39037400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr2:39024000-39053000	Weak transcription	Psoas Muscle	Psoas
38	chr2:39024200-39033000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr2:39024400-39034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr2:39024600-39033200	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:39025400-39032000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr2:39025400-39038000	Weak transcription	HUVEC	blood vessel
43	chr2:39025600-39032000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:39025600-39032000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:39025600-39037600	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:39025600-39042400	Weak transcription	Hela-S3	cervix
47	chr2:39025600-39042400	Weak transcription	HSMM	muscle
48	chr2:39025800-39032000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:39025800-39032200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr2:39025800-39032200	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links