Variant report

Variant	rs6440094
Chromosome Location	chr3:142316443-142316444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:142313766..142316499-chr3:142498136..142500635,2	K562	blood:
2	chr3:142294568..142300006-chr3:142310942..142319455,13	MCF-7	breast:
3	chr3:142313378..142316741-chr3:142442748..142446550,8	K562	blood:
4	chr3:142294183..142301262-chr3:142311308..142318922,13	MCF-7	breast:
5	chr3:142312229..142317018-chr3:142442889..142445391,9	K562	blood:
6	chr3:142314524..142316871-chr3:142442608..142445149,2	MCF-7	breast:
7	chr3:142314277..142316663-chr3:142382049..142384101,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144935	Chromatin interaction
ENSG00000120756	Chromatin interaction
ENSG00000242390	Chromatin interaction
ENSG00000175054	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10935465	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1129393	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13061823	0.91[CHB][hapmap]
rs13065075	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13067795	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13069307	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13079246	0.82[CEU][hapmap]
rs13085998	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13093869	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098343	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357529	0.89[EUR][1000 genomes]
rs1357530	0.93[CEU][hapmap];0.91[EUR][1000 genomes]
rs16852486	0.81[CEU][hapmap]
rs1916639	0.91[EUR][1000 genomes]
rs1983434	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs1983435	0.92[EUR][1000 genomes]
rs2030613	0.93[CEU][hapmap];0.82[JPT][hapmap];0.92[EUR][1000 genomes]
rs2049325	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs2049326	0.92[EUR][1000 genomes]
rs2140432	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs2177396	0.92[EUR][1000 genomes]
rs2227928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2227930	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2354860	0.90[EUR][1000 genomes]
rs28617475	0.80[ASN][1000 genomes]
rs2883380	0.81[CEU][hapmap]
rs3922730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4273389	0.84[EUR][1000 genomes]
rs4413348	0.92[CEU][hapmap];0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs4441672	0.92[CHB][hapmap]
rs4597728	0.83[EUR][1000 genomes]
rs4683688	0.81[CEU][hapmap]
rs4683690	0.82[CEU][hapmap]
rs6414350	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440086	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6440087	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6440088	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6440089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6440090	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440092	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440098	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs6440099	0.92[EUR][1000 genomes]
rs6768093	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6770155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772400	0.92[CHB][hapmap]
rs6775583	0.83[EUR][1000 genomes]
rs6775718	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6775813	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs6780250	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs6782400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6783203	0.92[EUR][1000 genomes]
rs6784089	0.92[EUR][1000 genomes]
rs6785675	0.82[EUR][1000 genomes]
rs6789958	0.81[CEU][hapmap]
rs6791816	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6792259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6793735	0.81[CEU][hapmap]
rs6798232	0.81[CEU][hapmap]
rs6799752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6802734	0.87[EUR][1000 genomes]
rs6802774	0.87[EUR][1000 genomes]
rs6808205	0.81[CEU][hapmap]
rs7428496	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7430429	0.81[CEU][hapmap]
rs7609842	0.85[EUR][1000 genomes]
rs7610557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615316	0.93[CEU][hapmap];0.92[EUR][1000 genomes]
rs7623524	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7630130	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7631313	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs7634158	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7635146	0.91[EUR][1000 genomes]
rs7641330	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7646880	0.92[EUR][1000 genomes]
rs7647573	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7651071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7651542	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9683085	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9808914	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9808943	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9816736	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs9820353	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9820770	0.82[EUR][1000 genomes]
rs9824176	0.86[EUR][1000 genomes]
rs9824893	0.92[EUR][1000 genomes]
rs9825207	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826786	0.86[CHB][hapmap]
rs9828178	0.82[EUR][1000 genomes]
rs9832606	0.82[CEU][hapmap]
rs9843148	0.87[CHB][hapmap]
rs9846960	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847364	0.91[CHB][hapmap]
rs9855140	0.84[EUR][1000 genomes]
rs9855919	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9862919	0.91[CEU][hapmap];0.81[JPT][hapmap]
rs9866958	0.92[CEU][hapmap];0.82[JPT][hapmap];0.91[EUR][1000 genomes]
rs9869842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9876254	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9879995	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9882763	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877556	chr3:141898980-142331360	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv877558	chr3:142123841-142331360	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv877559	chr3:142132749-142331360	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv877560	chr3:142132749-142362179	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' 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	35 gene(s)	inside rSNPs	diseases
5	nsv877561	chr3:142152925-142331360	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv932989	chr3:142204208-142423305	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:142314200-142317800	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr3:142314400-142316600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr3:142314400-142316800	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:142314400-142317200	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:142314400-142317400	Active TSS	Colonic Mucosa	Colon
6	chr3:142314400-142317400	Active TSS	Fetal Kidney	kidney
7	chr3:142314400-142317600	Active TSS	Rectal Smooth Muscle	rectum
8	chr3:142314400-142317800	Active TSS	Duodenum Mucosa	Duodenum
9	chr3:142314600-142317600	Active TSS	Stomach Mucosa	stomach
10	chr3:142314800-142316800	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr3:142314800-142316800	Active TSS	Rectal Mucosa Donor 31	rectum
12	chr3:142315600-142317000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:142315600-142317200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr3:142315600-142317400	Flanking Active TSS	Dnd41	blood
15	chr3:142315600-142319200	Weak transcription	Gastric	stomach
16	chr3:142315800-142316600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:142315800-142316600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:142315800-142316800	Weak transcription	Pancreas	Pancrea
19	chr3:142315800-142318000	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:142315800-142320400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:142315800-142324400	Weak transcription	Lung	lung
22	chr3:142316000-142316600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
23	chr3:142316000-142316600	Enhancers	Primary T cells from cord blood	blood
24	chr3:142316000-142316600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr3:142316000-142316600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:142316000-142316800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:142316000-142317000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:142316000-142317000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr3:142316000-142317200	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr3:142316000-142317200	Active TSS	Fetal Stomach	stomach
31	chr3:142316000-142317200	Flanking Active TSS	NHEK	skin
32	chr3:142316000-142317400	Enhancers	Fetal Thymus	thymus
33	chr3:142316000-142319800	Weak transcription	NH-A	brain
34	chr3:142316000-142321000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:142316000-142321600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:142316200-142316800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:142316200-142316800	Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:142316200-142316800	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr3:142316200-142316800	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr3:142316200-142317000	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:142316200-142317000	Flanking Active TSS	A549	lung
42	chr3:142316200-142317200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:142316200-142317200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:142316200-142317200	Enhancers	Thymus	Thymus
45	chr3:142316200-142317400	Enhancers	Liver	Liver
46	chr3:142316200-142317400	Enhancers	Hela-S3	cervix
47	chr3:142316200-142318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr3:142316200-142331000	Weak transcription	Small Intestine	intestine
49	chr3:142316400-142316600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr3:142316400-142316600	Flanking Active TSS	Primary hematopoietic stem cells	blood

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