Variant report

Variant	rs6932778
Chromosome Location	chr6:149649429-149649430
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149648554..149650974-chr6:149651371..149654134,3	K562	blood:
2	chr6:149636994..149642058-chr6:149649092..149655125,9	MCF-7	breast:
3	chr6:149643394..149646422-chr6:149647403..149650011,4	K562	blood:
4	chr6:149647673..149650092-chr6:149672445..149675357,2	K562	blood:
5	chr6:149642865..149645034-chr6:149649169..149650874,2	MCF-7	breast:
6	chr6:149644563..149647339-chr6:149647427..149650792,4	K562	blood:
7	chr6:149646598..149650161-chr6:149650268..149655691,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1001305	1.00[ASN][1000 genomes]
rs10155766	0.87[AFR][1000 genomes]
rs10872636	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11155640	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11155642	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs11155645	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11155646	0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11155647	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs11155654	1.00[ASN][1000 genomes]
rs12154153	0.87[AFR][1000 genomes]
rs12191079	0.80[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12192159	1.00[ASN][1000 genomes]
rs12192814	0.91[ASN][1000 genomes]
rs12195922	0.82[ASN][1000 genomes]
rs12196656	0.87[AFR][1000 genomes]
rs12197598	0.87[AFR][1000 genomes]
rs12204461	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs12204793	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12211357	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12211570	0.86[AFR][1000 genomes]
rs17506789	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1980774	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs34097428	0.87[AFR][1000 genomes]
rs4493763	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs537354	0.81[YRI][hapmap]
rs55826712	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56924465	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs58747890	1.00[ASN][1000 genomes]
rs59820585	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs60153446	0.87[AFR][1000 genomes]
rs61259243	0.87[AFR][1000 genomes]
rs62426068	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62426069	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62426088	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs62426092	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62426115	0.87[AFR][1000 genomes]
rs62441727	1.00[ASN][1000 genomes]
rs638407	0.81[YRI][hapmap]
rs66672129	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs68080376	0.84[AFR][1000 genomes]
rs6911411	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6920383	0.85[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7349921	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs763590	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs7741099	1.00[ASN][1000 genomes]
rs7747354	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];1.00[ASN][1000 genomes]
rs7747948	1.00[ASN][1000 genomes]
rs7762222	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7896	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs9285520	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9322178	0.81[YRI][hapmap]
rs9373589	0.81[YRI][hapmap]
rs9390677	0.80[YRI][hapmap]
rs9485385	0.91[ASN][1000 genomes]
rs9485392	1.00[ASN][1000 genomes]
rs9485394	0.91[ASN][1000 genomes]
rs9485397	1.00[ASN][1000 genomes]
rs9498322	0.84[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9498323	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9498324	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9498325	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9498328	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9498329	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9498330	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9498332	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498333	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498334	0.85[AFR][1000 genomes]
rs9498335	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498336	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498337	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498338	0.82[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498341	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498342	0.84[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs9498344	0.87[AFR][1000 genomes]
rs9498349	0.91[ASN][1000 genomes]
rs9498351	0.91[ASN][1000 genomes]
rs9498352	1.00[ASN][1000 genomes]
rs9498353	1.00[ASN][1000 genomes]
rs9498354	1.00[ASN][1000 genomes]
rs9498355	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs9498356	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs9498358	1.00[ASN][1000 genomes]
rs997682	0.84[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1015360	chr6:149609804-149649982	Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1024106	chr6:149622349-149745053	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	10 gene(s)	inside rSNPs	diseases
4	nsv522875	chr6:149643709-149762537	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149640200-149655400	Weak transcription	Esophagus	oesophagus
2	chr6:149640200-149655600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:149640800-149652800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr6:149640800-149653200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:149641200-149657400	Weak transcription	Aorta	Aorta
6	chr6:149641200-149681400	Weak transcription	Fetal Stomach	stomach
7	chr6:149641400-149655600	Weak transcription	Placenta	Placenta
8	chr6:149641600-149652600	Weak transcription	Brain Germinal Matrix	brain
9	chr6:149641600-149656000	Weak transcription	Lung	lung
10	chr6:149641600-149660200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:149641800-149660200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr6:149642200-149652000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:149642400-149650200	Weak transcription	Primary B cells from cord blood	blood
14	chr6:149642400-149652600	Weak transcription	NH-A	brain
15	chr6:149642400-149652600	Weak transcription	NHLF	lung
16	chr6:149642600-149652600	Weak transcription	NHDF-Ad	bronchial
17	chr6:149642600-149657200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:149642800-149650400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr6:149643000-149653400	Weak transcription	HSMM	muscle
20	chr6:149643400-149652200	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr6:149645000-149666400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr6:149645200-149649800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:149645600-149652600	Weak transcription	Osteobl	bone
24	chr6:149645800-149651800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr6:149645800-149651800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr6:149645800-149652800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr6:149646000-149651400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:149646000-149652600	Weak transcription	HMEC	breast
29	chr6:149646200-149650400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr6:149646200-149650400	Weak transcription	Fetal Thymus	thymus
31	chr6:149646200-149653400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:149646200-149654400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr6:149646200-149657400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:149646400-149652600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:149646400-149652600	Weak transcription	Adipose Nuclei	Adipose
36	chr6:149646400-149652600	Weak transcription	Fetal Lung	lung
37	chr6:149646600-149652800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:149646800-149652400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr6:149647000-149653000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr6:149647200-149649800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr6:149647200-149649800	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr6:149647200-149650000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:149647200-149650200	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:149647200-149650400	Weak transcription	Stomach Mucosa	stomach
45	chr6:149647200-149651400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:149647200-149653000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr6:149647200-149654400	Weak transcription	Ovary	ovary
48	chr6:149647200-149655400	Weak transcription	Pancreas	Pancrea
49	chr6:149647800-149650400	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr6:149647800-149651600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links