Variant report

Variant	rs4848971
Chromosome Location	chr2:112790446-112790447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112786053..112788875-chr2:112788955..112792026,3	K562	blood:
2	chr2:112654547..112656932-chr2:112789072..112792767,3	MCF-7	breast:
3	chr2:112782602..112784298-chr2:112789398..112791163,2	K562	blood:

Variant related genes	Relation type
ENSG00000153208	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10169022	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10176660	0.85[ASN][1000 genomes]
rs10176769	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs10192728	0.89[CEU][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs10194496	0.82[JPT][hapmap]
rs10207301	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10496439	0.88[CEU][hapmap]
rs1122970	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11673729	0.88[CEU][hapmap]
rs11674226	0.92[CEU][hapmap]
rs11674883	0.92[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs11674891	0.92[CEU][hapmap]
rs11675946	0.84[CEU][hapmap];0.80[TSI][hapmap]
rs11679125	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11679593	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11679801	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11680463	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11681063	0.83[EUR][1000 genomes]
rs11682629	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11683694	0.92[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11684321	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11684476	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11685190	0.92[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11687451	0.92[CEU][hapmap];0.92[TSI][hapmap]
rs11690440	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692445	0.92[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs11897014	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12995767	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13001162	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13003919	0.92[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13006203	0.88[CEU][hapmap]
rs13006228	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020304	0.92[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs13020353	0.82[EUR][1000 genomes]
rs13024271	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13025651	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13027171	0.92[CEU][hapmap];0.92[TSI][hapmap]
rs13033393	0.92[CEU][hapmap]
rs1554216	0.92[CEU][hapmap]
rs17174697	0.88[CEU][hapmap]
rs17779482	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs2271701	0.92[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs34128716	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34240639	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34527376	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34593596	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34705448	0.83[EUR][1000 genomes]
rs34875611	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35189728	0.83[EUR][1000 genomes]
rs35379879	0.83[EUR][1000 genomes]
rs35382200	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35643003	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35757708	0.86[EUR][1000 genomes]
rs3761699	0.92[CEU][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs3811633	0.92[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3811634	0.92[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4264571	0.88[CEU][hapmap]
rs4318395	0.81[CEU][hapmap]
rs4575728	0.86[ASN][1000 genomes]
rs4632347	0.82[JPT][hapmap]
rs4848229	0.92[CEU][hapmap]
rs4848238	0.92[CEU][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4848241	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4848861	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs4848874	0.92[CEU][hapmap]
rs4848899	0.83[EUR][1000 genomes]
rs4848958	0.84[ASN][1000 genomes]
rs4848973	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4848975	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4848979	0.89[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs4848980	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704665	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6722814	0.89[CEU][hapmap];0.92[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6736093	0.88[CEU][hapmap];0.92[TSI][hapmap]
rs6743523	0.92[CEU][hapmap]
rs6748256	0.92[JPT][hapmap]
rs6754526	0.83[EUR][1000 genomes]
rs72829613	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7349221	0.88[CEU][hapmap]
rs7578435	0.83[EUR][1000 genomes]
rs7586558	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7595212	0.88[CEU][hapmap]
rs7604403	0.88[CEU][hapmap];0.87[TSI][hapmap]
rs870761	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs870763	0.92[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][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	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv999746	chr2:112691270-112796083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv2760607	chr2:112691282-112803423	Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv431491	chr2:112699350-112793981	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv515698	chr2:112699350-112795908	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv933392	chr2:112747230-112792349	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1793068	chr2:112784234-112816694	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4848971	TMEM87B	cis	parietal	SCAN
rs4848971	FBLN7	cis	parietal	SCAN
rs4848971	MERTK	cis	multi-tissue	Pritchard

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112713200-112790600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:112769600-112791200	Weak transcription	Colonic Mucosa	Colon
3	chr2:112781600-112790600	Weak transcription	Lung	lung
4	chr2:112783000-112790600	Weak transcription	Pancreas	Pancrea
5	chr2:112783200-112790600	Weak transcription	Esophagus	oesophagus
6	chr2:112783200-112802200	Weak transcription	Aorta	Aorta
7	chr2:112786200-112790600	Weak transcription	Left Ventricle	heart
8	chr2:112786200-112790600	Weak transcription	Stomach Mucosa	stomach
9	chr2:112786200-112798800	Weak transcription	K562	blood
10	chr2:112786400-112790600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:112786400-112796000	Weak transcription	Gastric	stomach
12	chr2:112789000-112790800	Enhancers	Fetal Intestine Small	intestine
13	chr2:112789000-112790800	Enhancers	Small Intestine	intestine
14	chr2:112789000-112791000	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:112789000-112791400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:112789000-112791400	Enhancers	Fetal Intestine Large	intestine
17	chr2:112789000-112791600	Enhancers	Placenta Amnion	Placenta Amnion
18	chr2:112789000-112792000	Enhancers	Duodenum Mucosa	Duodenum
19	chr2:112789000-112792000	Enhancers	HUVEC	blood vessel
20	chr2:112789000-112792600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr2:112789000-112792600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:112789200-112790800	Enhancers	Liver	Liver
23	chr2:112789200-112790800	Enhancers	Placenta	Placenta
24	chr2:112789200-112790800	Enhancers	Fetal Thymus	thymus
25	chr2:112789200-112790800	Flanking Active TSS	Dnd41	blood
26	chr2:112789200-112790800	Enhancers	HepG2	liver
27	chr2:112789200-112791400	Enhancers	Fetal Stomach	stomach
28	chr2:112789200-112791600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:112789200-112791600	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr2:112789200-112791600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:112789200-112791600	Enhancers	Brain Hippocampus Middle	brain
32	chr2:112789200-112791600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:112789200-112792000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr2:112789200-112792000	Enhancers	Colon Smooth Muscle	Colon
35	chr2:112789400-112790800	Enhancers	GM12878-XiMat	blood
36	chr2:112789400-112791200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
37	chr2:112789400-112791400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr2:112789600-112790800	Enhancers	Fetal Muscle Leg	muscle
39	chr2:112789600-112791000	Enhancers	Stomach Smooth Muscle	stomach
40	chr2:112789600-112792000	Enhancers	NHLF	lung
41	chr2:112789800-112790600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr2:112789800-112790600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:112789800-112790800	Enhancers	Adipose Nuclei	Adipose
44	chr2:112789800-112790800	Enhancers	Fetal Lung	lung
45	chr2:112789800-112790800	Enhancers	HSMMtube	muscle
46	chr2:112789800-112791200	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr2:112789800-112791400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr2:112789800-112791400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:112789800-112791800	Enhancers	Osteobl	bone
50	chr2:112789800-112792000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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