Variant report

Variant	rs9498204
Chromosome Location	chr6:149404346-149404347
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:149403185..149406619-chr6:149636459..149640490,6	MCF-7	breast:
2	chr6:149376456..149387248-chr6:149393069..149406749,44	MCF-7	breast:
3	chr6:149351101..149353287-chr6:149403711..149405332,2	MCF-7	breast:
4	chr6:149404330..149406131-chr6:149751650..149753242,2	MCF-7	breast:
5	chr6:149400690..149404463-chr6:149557705..149560765,3	MCF-7	breast:
6	chr6:149403546..149405642-chr6:149411704..149413513,2	MCF-7	breast:
7	chr6:149402943..149406251-chr6:149407231..149409997,4	K562	blood:
8	chr6:149400900..149408936-chr6:149636750..149640736,16	MCF-7	breast:
9	chr6:149403286..149404899-chr6:149752639..149753736,6	MCF-7	breast:
10	chr6:149400971..149403372-chr6:149403878..149405547,2	K562	blood:
11	chr6:149403345..149406276-chr6:149836052..149838549,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction
ENSG00000252244	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10457075	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10457839	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10457842	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10499251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12153925	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12196284	1.00[JPT][hapmap]
rs12197040	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12200909	0.91[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12202158	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12206419	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1316376	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13190879	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13217006	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17669546	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1890610	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1890612	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1934221	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1934222	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1934223	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2153251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153252	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2185250	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34118116	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34599887	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3949414	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4313020	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4332004	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4336467	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4441968	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4454159	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6570921	0.82[GIH][hapmap]
rs6570923	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6570924	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6570926	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6570927	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6570932	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6900527	1.00[JPT][hapmap]
rs6901626	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902195	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6902487	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6909527	1.00[JPT][hapmap]
rs6909624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6914281	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6914318	0.85[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6914925	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6917010	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6924503	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6930713	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6932773	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6940664	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6940915	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7762928	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7773409	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7776204	1.00[JPT][hapmap]
rs9322165	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9390652	0.85[GIH][hapmap]
rs9485353	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9498197	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9498199	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9498201	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9498202	0.88[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9498205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9498207	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830842	chr6:149272321-149427340	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	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
5	nsv528588	chr6:149403469-149409860	Weak transcription Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149395000-149415000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:149397800-149407600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr6:149399200-149415000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:149400200-149406000	Enhancers	Dnd41	blood
5	chr6:149400600-149406800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr6:149402200-149405200	Weak transcription	Fetal Thymus	thymus
7	chr6:149402200-149405200	Weak transcription	Pancreas	Pancrea
8	chr6:149402200-149407000	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr6:149402200-149409000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:149402200-149410600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:149402200-149414400	Weak transcription	Fetal Kidney	kidney
12	chr6:149402200-149414600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr6:149402200-149415000	Weak transcription	Esophagus	oesophagus
14	chr6:149402400-149407800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr6:149402400-149409000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr6:149402400-149416200	Weak transcription	Fetal Heart	heart
17	chr6:149402600-149406000	Weak transcription	Aorta	Aorta
18	chr6:149402800-149407000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:149403000-149407200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:149403200-149405600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr6:149403200-149406600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr6:149403200-149407200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr6:149403200-149407600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr6:149403400-149404600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr6:149403400-149405600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr6:149403400-149406200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr6:149403400-149406200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr6:149403600-149404400	Enhancers	Brain Anterior Caudate	brain
29	chr6:149403600-149404400	Enhancers	Brain Cingulate Gyrus	brain
30	chr6:149403600-149404400	Enhancers	Brain Substantia Nigra	brain
31	chr6:149403600-149404800	Enhancers	Fetal Lung	lung
32	chr6:149403600-149405600	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:149403600-149405800	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr6:149403600-149406200	Enhancers	Primary T cells from cord blood	blood
35	chr6:149403600-149406200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr6:149403600-149407200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr6:149403800-149404600	Enhancers	Brain Hippocampus Middle	brain
38	chr6:149404200-149404400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:149404200-149404400	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr6:149404200-149404400	Enhancers	Rectal Smooth Muscle	rectum
41	chr6:149404200-149404600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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