Variant report

Variant	rs4140802
Chromosome Location	chr7:7727975-7727976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:7726921..7729917-chr7:7734737..7737606,4	K562	blood:
2	chr7:7726990..7730835-chr7:7733488..7736848,3	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10229371	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10262410	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10263415	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10264890	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10277292	0.83[GIH][hapmap];0.82[MKK][hapmap]
rs10277945	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11508478	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11773013	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs11773126	0.92[CHB][hapmap]
rs13232471	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13234728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13239834	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13246995	1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1468762	0.85[ASN][1000 genomes]
rs17169379	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057929	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057930	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2057931	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2108001	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2108003	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2158715	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2160138	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs2881961	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4140804	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4140805	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4720750	0.92[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs4725014	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6966726	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967126	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7791564	0.89[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7805143	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7805802	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886725	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs886726	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9640047	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026758	chr7:7187491-8075259	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
2	nsv606042	chr7:7427535-7876466	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv887477	chr7:7531819-7810122	Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1032670	chr7:7535515-8017077	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv8043	chr7:7589195-7862802	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv887478	chr7:7670718-7917360	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv887479	chr7:7681131-7779091	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv887480	chr7:7681131-7917360	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv887481	chr7:7681576-7779324	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv887482	chr7:7682439-7785047	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv887483	chr7:7682439-7798217	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv887484	chr7:7692483-7769363	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv887485	chr7:7692483-7917360	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv606045	chr7:7704889-7755491	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv887486	chr7:7712498-7785047	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4140802	MIOS	cis	cerebellum	SCAN
rs4140802	PMS2	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:7706800-7743200	Weak transcription	Gastric	stomach
2	chr7:7708600-7738600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:7715800-7728800	Weak transcription	Right Ventricle	heart
4	chr7:7715800-7736400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr7:7716000-7733400	Weak transcription	Esophagus	oesophagus
6	chr7:7716000-7735200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:7716000-7738400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:7717800-7749000	Weak transcription	Fetal Intestine Small	intestine
9	chr7:7718000-7731400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr7:7721200-7734800	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:7721400-7733000	Weak transcription	Osteobl	bone
12	chr7:7721600-7731800	Weak transcription	A549	lung
13	chr7:7721600-7733400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:7721600-7748800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr7:7721800-7728800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr7:7721800-7728800	Weak transcription	HSMM	muscle
17	chr7:7721800-7734400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr7:7721800-7737000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr7:7722000-7750600	Weak transcription	Primary B cells from cord blood	blood
20	chr7:7722600-7744400	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr7:7722600-7745600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr7:7722800-7733600	Weak transcription	Hela-S3	cervix
23	chr7:7722800-7738600	Weak transcription	GM12878-XiMat	blood
24	chr7:7722800-7742400	Weak transcription	Pancreas	Pancrea
25	chr7:7723000-7728000	Weak transcription	NHEK	skin
26	chr7:7723000-7729000	Weak transcription	Brain Hippocampus Middle	brain
27	chr7:7723000-7733600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:7725600-7729000	Enhancers	Fetal Thymus	thymus
29	chr7:7725600-7729000	Enhancers	Thymus	Thymus
30	chr7:7726400-7728000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr7:7726400-7728000	Enhancers	Adipose Nuclei	Adipose
32	chr7:7726600-7729400	Enhancers	Muscle Satellite Cultured Cells	--
33	chr7:7726800-7731600	Weak transcription	Primary T cells from cord blood	blood
34	chr7:7726800-7737600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:7726800-7745800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr7:7727000-7728000	Enhancers	Psoas Muscle	Psoas
37	chr7:7727000-7728200	Enhancers	HUVEC	blood vessel
38	chr7:7727000-7734800	Weak transcription	Brain Substantia Nigra	brain
39	chr7:7727200-7728600	Active TSS	Stomach Smooth Muscle	stomach
40	chr7:7727200-7728600	Weak transcription	Spleen	Spleen
41	chr7:7727200-7730600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:7727200-7734400	Weak transcription	Brain Anterior Caudate	brain
43	chr7:7727200-7734800	Weak transcription	Rectal Smooth Muscle	rectum
44	chr7:7727400-7728000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr7:7727600-7728200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:7727600-7728200	Enhancers	Stomach Mucosa	stomach
47	chr7:7727600-7728400	Active TSS	Aorta	Aorta
48	chr7:7727600-7728600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr7:7727600-7729000	Enhancers	Primary B cells from peripheral blood	blood
50	chr7:7727600-7741000	Weak transcription	Brain Germinal Matrix	brain

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