Variant report

Variant	rs335963
Chromosome Location	chr6:2248825-2248826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:2244284..2246271-chr6:2246300..2249565,3	K562	blood:
2	chr6:2248443..2250050-chr6:2251800..2254441,2	MCF-7	breast:
3	chr6:2244284..2247491-chr6:2247756..2249566,3	K562	blood:

Variant related genes	Relation type
ENSG00000250903	Chromatin interaction
ENSG00000112699	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1196389	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196390	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196393	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196394	0.92[ASN][1000 genomes]
rs1196396	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529910	0.86[JPT][hapmap]
rs1475411	0.88[AMR][1000 genomes]
rs1486274	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1629950	0.92[ASN][1000 genomes]
rs1684153	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1887418	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1887420	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2148824	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs234920	0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs2450301	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2450303	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2450306	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2450311	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2478999	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2479000	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2479003	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2479005	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2479009	0.86[AMR][1000 genomes]
rs2479010	0.88[AMR][1000 genomes]
rs2479012	0.87[AMR][1000 genomes]
rs2479015	0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.93[ASN][1000 genomes]
rs2479016	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2505656	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2505665	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2505668	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2505669	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2505672	0.87[AMR][1000 genomes]
rs2505674	0.87[AMR][1000 genomes]
rs4959648	0.87[AMR][1000 genomes]
rs62392643	0.87[AMR][1000 genomes]
rs6596876	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6939099	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7765735	0.87[AMR][1000 genomes]
rs7766115	0.87[AMR][1000 genomes]
rs9328086	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9392379	0.87[AMR][1000 genomes]
rs9392382	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9405552	0.82[AMR][1000 genomes]
rs9501828	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv531295	chr6:1773436-2724986	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
3	nsv1025814	chr6:2064629-2308518	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538098	chr6:2064629-2308518	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv1030181	chr6:2071210-2308657	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv538099	chr6:2071210-2308657	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv883388	chr6:2093432-2514911	Strong transcription Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
8	nsv883389	chr6:2093432-2776303	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
9	nsv830573	chr6:2120985-2263646	Bivalent Enhancer Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
10	nsv1022623	chr6:2199666-2267750	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv538100	chr6:2199666-2267750	ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv1022166	chr6:2199666-2320800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
13	nsv1017174	chr6:2213893-2340529	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv1033201	chr6:2218647-2308518	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers 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	41 gene(s)	inside rSNPs	diseases
15	nsv538101	chr6:2218647-2308518	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
16	nsv1026678	chr6:2230064-2261297	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	n/a
17	esv2763526	chr6:2230064-2311916	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
18	nsv1021573	chr6:2246721-2832408	Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
19	nsv538102	chr6:2246721-2832408	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:2246800-2249000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:2246800-2249000	Weak transcription	Ovary	ovary
3	chr6:2246800-2250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr6:2246800-2250800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr6:2246800-2254800	Weak transcription	Esophagus	oesophagus
6	chr6:2246800-2255800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:2246800-2264200	Weak transcription	Gastric	stomach
8	chr6:2247000-2249000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:2247000-2249000	Weak transcription	Left Ventricle	heart
10	chr6:2247000-2249200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:2247000-2249200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:2247000-2249200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:2247000-2249200	Weak transcription	Fetal Stomach	stomach
14	chr6:2247000-2249400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr6:2247000-2249400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr6:2247000-2249400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:2247000-2249400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr6:2247000-2249600	Weak transcription	Brain Angular Gyrus	brain
19	chr6:2247000-2249600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:2247000-2250000	Weak transcription	Lung	lung
21	chr6:2247000-2250200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr6:2247000-2250200	Weak transcription	Aorta	Aorta
23	chr6:2247000-2253200	Weak transcription	Psoas Muscle	Psoas
24	chr6:2247000-2253800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr6:2247000-2254600	Weak transcription	Brain Substantia Nigra	brain
26	chr6:2247000-2254600	Weak transcription	Spleen	Spleen
27	chr6:2247000-2254600	Weak transcription	HSMM	muscle
28	chr6:2247000-2254800	Weak transcription	Brain Hippocampus Middle	brain
29	chr6:2247000-2254800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:2247000-2255200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:2247000-2255400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr6:2247000-2258600	Weak transcription	Colonic Mucosa	Colon
33	chr6:2247000-2260400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:2247000-2264200	Weak transcription	Brain Cingulate Gyrus	brain
35	chr6:2247000-2264400	Weak transcription	HSMMtube	muscle
36	chr6:2247000-2264800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:2247000-2265200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr6:2247000-2265200	Weak transcription	Osteobl	bone
39	chr6:2247000-2269400	Weak transcription	Right Ventricle	heart
40	chr6:2247000-2273800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr6:2247000-2275000	Weak transcription	Fetal Kidney	kidney
42	chr6:2247000-2275400	Weak transcription	NHLF	lung
43	chr6:2247000-2275600	Weak transcription	Fetal Heart	heart
44	chr6:2247200-2249000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr6:2247200-2249000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr6:2247200-2249000	Weak transcription	Liver	Liver
47	chr6:2247200-2249200	Weak transcription	Adipose Nuclei	Adipose
48	chr6:2247200-2249200	Weak transcription	Brain Anterior Caudate	brain
49	chr6:2247200-2249200	Weak transcription	Fetal Muscle Leg	muscle
50	chr6:2247200-2249400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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