Variant report

Variant	rs6847397
Chromosome Location	chr4:128569904-128569905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:128564328..128566993-chr4:128568354..128570269,2	MCF-7	breast:
2	chr4:128552418..128557041-chr4:128564673..128569925,6	K562	blood:

Variant related genes	Relation type
ENSG00000164066	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1018289	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098931	1.00[CEU][hapmap];0.81[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11098933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11728750	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11732886	0.92[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[MKK][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509562	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12511932	0.93[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12649427	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12650360	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13126673	0.85[CEU][hapmap]
rs13151291	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1399210	0.86[EUR][1000 genomes]
rs1399211	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1459049	0.81[CEU][hapmap]
rs1459051	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1514298	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1514299	0.89[CEU][hapmap];0.85[GIH][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1913464	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2048685	0.85[EUR][1000 genomes]
rs2048686	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2125573	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs2255457	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2391188	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2391189	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28656192	0.88[EUR][1000 genomes]
rs34240473	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36179490	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749507	0.89[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs4543128	0.85[CEU][hapmap]
rs4833383	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs4834206	0.86[EUR][1000 genomes]
rs4834209	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4834210	0.81[CEU][hapmap]
rs4834211	0.85[CEU][hapmap];0.84[GIH][hapmap]
rs59255549	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62334037	0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6534630	0.86[EUR][1000 genomes]
rs6534631	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6534632	0.89[CEU][hapmap];0.82[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs6534633	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534634	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6534637	0.85[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6810904	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823957	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6828511	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6847056	0.85[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs6858855	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7664217	0.87[EUR][1000 genomes]
rs7679782	0.84[EUR][1000 genomes]
rs7683627	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7686395	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7692114	0.89[CEU][hapmap]
rs922060	0.92[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv879915	chr4:128167093-129150590	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1029214	chr4:128292215-128683123	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537247	chr4:128292215-128683123	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817326	chr4:128292216-128915201	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv879916	chr4:128422400-128694288	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv879917	chr4:128478408-128841252	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv830056	chr4:128517139-128676557	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv879918	chr4:128543742-128694288	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv879919	chr4:128543742-128697519	Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
10	nsv879920	chr4:128554404-128694288	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv879921	chr4:128554404-128766074	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv879922	chr4:128554404-128901402	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
13	nsv879923	chr4:128554404-129068179	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
14	nsv879924	chr4:128566686-128622430	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
15	esv1801492	chr4:128566686-128934513	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	esv1792644	chr4:128566686-129133826	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	esv1795770	chr4:128566686-129145581	Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6847397	HSPA4L	cis	cerebellum	SCAN
rs6847397	PGRMC2	cis	cerebellum	SCAN
rs6847397	LARP1B	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:128554600-128627400	Weak transcription	Pancreas	Pancrea
2	chr4:128554600-128644800	Weak transcription	Lung	lung
3	chr4:128554800-128596600	Weak transcription	Fetal Muscle Leg	muscle
4	chr4:128554800-128604400	Weak transcription	Right Ventricle	heart
5	chr4:128555000-128570000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:128555000-128579400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:128555000-128608800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr4:128555200-128577000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:128555200-128577000	Weak transcription	A549	lung
10	chr4:128555200-128577200	Weak transcription	HepG2	liver
11	chr4:128555200-128577400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:128555200-128578600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr4:128555200-128586000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr4:128555200-128587400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr4:128555600-128577200	Weak transcription	K562	blood
16	chr4:128555600-128627600	Weak transcription	Brain Angular Gyrus	brain
17	chr4:128556200-128590200	Weak transcription	NH-A	brain
18	chr4:128556200-128615600	Weak transcription	Fetal Brain Male	brain
19	chr4:128559400-128583000	Weak transcription	Liver	Liver
20	chr4:128562400-128582600	Weak transcription	Spleen	Spleen
21	chr4:128562800-128578000	Weak transcription	Adipose Nuclei	Adipose
22	chr4:128562800-128581400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr4:128562800-128597400	Weak transcription	Esophagus	oesophagus
24	chr4:128562800-128616400	Weak transcription	Aorta	Aorta
25	chr4:128563000-128570200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:128563600-128614000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr4:128563600-128627400	Weak transcription	Brain Substantia Nigra	brain
28	chr4:128564000-128574200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:128565200-128578600	Weak transcription	Gastric	stomach
30	chr4:128565400-128572400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr4:128565400-128577400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:128565400-128587600	Weak transcription	Brain Cingulate Gyrus	brain
33	chr4:128565400-128592800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:128565400-128615400	Weak transcription	Colon Smooth Muscle	Colon
35	chr4:128566400-128577000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:128566600-128570000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:128566600-128570000	Weak transcription	Fetal Lung	lung
38	chr4:128566600-128571000	Weak transcription	Osteobl	bone
39	chr4:128566600-128577000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr4:128566600-128579200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:128566600-128582800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr4:128566600-128584800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr4:128566600-128589200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr4:128566600-128590000	Weak transcription	Fetal Kidney	kidney
45	chr4:128566600-128590000	Weak transcription	HSMM	muscle
46	chr4:128566600-128596600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:128566600-128644600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:128567000-128571000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:128567000-128597400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr4:128567200-128614000	Weak transcription	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links