Variant report

Variant	rs199750
Chromosome Location	chr6:26016462-26016463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:26016425-26017408	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25991481..25993438-chr6:26015538..26017595,2	MCF-7	breast:

Variant related genes	Relation type
HIST1H3A	TF binding region
HIST1H1PS2	TF binding region
ENSG00000272462	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10425	0.96[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs115810	0.96[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1165201	0.87[CHD][hapmap]
rs12346	0.86[ASW][hapmap];0.91[CEU][hapmap];0.96[CHD][hapmap];0.81[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.88[AFR][1000 genomes]
rs129129	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap]
rs1540275	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1540276	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs169219	0.84[CHD][hapmap];0.81[GIH][hapmap]
rs175319	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1935235	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs198810	0.88[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs198815	0.86[JPT][hapmap]
rs198820	0.88[CHD][hapmap];0.83[GIH][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap]
rs198845	0.96[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs198848	0.96[CHD][hapmap];0.83[GIH][hapmap];0.90[MEX][hapmap]
rs198852	0.96[CHD][hapmap];0.83[GIH][hapmap]
rs198853	0.91[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs199734	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs199737	0.86[CHB][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs199739	0.86[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs199741	0.84[ASW][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.88[LWK][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap]
rs199751	1.00[CEU][hapmap];0.86[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];0.95[ASN][1000 genomes]
rs199752	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs199753	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs199754	1.00[ASW][hapmap];0.91[CEU][hapmap];0.86[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs199755	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2032447	0.92[CEU][hapmap];0.92[CHD][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2213284	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2230655	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34413295	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3752416	0.83[EUR][1000 genomes]
rs428469	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs4401650	0.92[CEU][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs442601	0.86[CHB][hapmap]
rs537581	0.87[CHD][hapmap];0.81[LWK][hapmap]
rs599444	0.87[CHD][hapmap];0.81[LWK][hapmap]
rs6901039	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922788	0.86[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6942072	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7756117	0.92[CEU][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7760848	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs807205	0.86[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs807212	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs807214	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9356995	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9356996	0.82[ASN][1000 genomes]
rs9358901	0.92[CEU][hapmap];0.88[CHB][hapmap];0.85[EUR][1000 genomes]
rs9467664	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription 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	1215 gene(s)	inside rSNPs	diseases
3	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
4	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
5	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
6	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv432857	chr6:25957109-26072445	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	451 gene(s)	inside rSNPs	diseases
8	nsv1015627	chr6:25973495-26100483	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
9	nsv538164	chr6:25973495-26100483	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	447 gene(s)	inside rSNPs	diseases
10	nsv1028456	chr6:25984457-26174993	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
11	nsv538165	chr6:25984457-26174993	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	873 gene(s)	inside rSNPs	diseases
12	nsv428137	chr6:25987413-26351920	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1181 gene(s)	inside rSNPs	diseases
13	nsv916992	chr6:25991630-26280921	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1159 gene(s)	inside rSNPs	diseases
14	nsv1028232	chr6:26005449-26319756	Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1171 gene(s)	inside rSNPs	diseases
15	nsv870314	chr6:26008435-26280807	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1151 gene(s)	inside rSNPs	diseases
16	nsv1023457	chr6:26014014-26305407	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1170 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs199750	HIST1H2BB	cis	parietal	SCAN
rs199750	HIST1H4I	cis	cerebellum	SCAN
rs199750	ZNF187	cis	parietal	SCAN
rs199750	HIST1H2BD	cis	multi-tissue	Pritchard
rs199750	HIST1H1T	cis	multi-tissue	Pritchard
rs199750	HIST1H2AJ	cis	parietal	SCAN
rs199750	HIST1H2AA	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25993600-26016600	Weak transcription	Aorta	Aorta
2	chr6:25999200-26016600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr6:25999200-26016600	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:25999200-26017200	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr6:25999400-26016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:25999400-26016600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:25999400-26016600	Weak transcription	Pancreas	Pancrea
8	chr6:25999400-26017400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr6:25999600-26016800	Weak transcription	Colon Smooth Muscle	Colon
10	chr6:25999800-26016600	Weak transcription	Esophagus	oesophagus
11	chr6:26001200-26016800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:26001600-26017600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr6:26001600-26020600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:26005400-26016600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:26005400-26017200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr6:26008800-26020600	Weak transcription	Spleen	Spleen
17	chr6:26015400-26016600	Enhancers	H1 Cell Line	embryonic stem cell
18	chr6:26015800-26016600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:26016000-26016600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr6:26016000-26016600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr6:26016200-26016600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr6:26016200-26016600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr6:26016200-26016600	Enhancers	Fetal Brain Male	brain
24	chr6:26016200-26016800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr6:26016200-26016800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:26016200-26017600	Active TSS	Fetal Lung	lung
27	chr6:26016200-26018400	Flanking Active TSS	Fetal Muscle Leg	muscle
28	chr6:26016200-26018600	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr6:26016200-26019800	Active TSS	Fetal Kidney	kidney
30	chr6:26016400-26016600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr6:26016400-26016600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
32	chr6:26016400-26016600	Flanking Active TSS	Fetal Heart	heart
33	chr6:26016400-26016600	Active TSS	Fetal Muscle Trunk	muscle
34	chr6:26016400-26016600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr6:26016400-26016600	Enhancers	HMEC	breast
36	chr6:26016400-26016600	Enhancers	HUVEC	blood vessel
37	chr6:26016400-26016600	Enhancers	NHEK	skin
38	chr6:26016400-26016600	Enhancers	Osteobl	bone
39	chr6:26016400-26016800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:26016400-26016800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr6:26016400-26016800	Flanking Active TSS	Fetal Intestine Large	intestine
42	chr6:26016400-26016800	Flanking Active TSS	Fetal Stomach	stomach
43	chr6:26016400-26017000	Flanking Active TSS	Liver	Liver
44	chr6:26016400-26017000	Active TSS	Fetal Brain Female	brain
45	chr6:26016400-26017400	Flanking Active TSS	Brain Germinal Matrix	brain
46	chr6:26016400-26017400	Flanking Active TSS	NH-A	brain
47	chr6:26016400-26017400	Active TSS	NHLF	lung
48	chr6:26016400-26017600	Active TSS	Right Ventricle	heart
49	chr6:26016400-26017800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:26016400-26017800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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