Variant report

Variant	rs6731661
Chromosome Location	chr2:54821704-54821705
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54782515..54784267-chr2:54820223..54822640,2	MCF-7	breast:
2	chr2:54785168..54787003-chr2:54819314..54822161,2	K562	blood:
3	chr2:54815707..54819448-chr2:54820160..54824681,7	K562	blood:
4	chr2:54815000..54820095-chr2:54820709..54825309,10	K562	blood:

Variant related genes	Relation type
ENSG00000115306	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10180713	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1047499	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11885703	0.85[EUR][1000 genomes]
rs11892788	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12104998	0.86[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12105792	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs12467581	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12468469	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12617036	0.87[EUR][1000 genomes]
rs12713260	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13016942	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs1367295	0.86[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1510611	0.87[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs1541854	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs168506	0.80[EUR][1000 genomes]
rs171350	0.82[EUR][1000 genomes]
rs17344072	0.82[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs17521078	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs1802889	1.00[YRI][hapmap]
rs1864493	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2048371	0.82[EUR][1000 genomes]
rs2271322	0.85[EUR][1000 genomes]
rs2292356	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2292357	0.90[EUR][1000 genomes]
rs2931463	0.85[EUR][1000 genomes]
rs2931464	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2941583	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2941586	0.95[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2941587	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2941591	0.86[EUR][1000 genomes]
rs2941595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2971875	0.81[EUR][1000 genomes]
rs2971877	0.95[CEU][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2971879	0.95[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2971883	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2971887	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3106204	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs354213	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs354223	0.81[AMR][1000 genomes]
rs354226	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs354228	0.83[EUR][1000 genomes]
rs354231	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3796014	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4233952	0.83[EUR][1000 genomes]
rs4444573	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4455199	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4519562	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4592889	0.89[EUR][1000 genomes]
rs4671221	0.81[CEU][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes]
rs4671222	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs4671225	0.89[EUR][1000 genomes]
rs4671226	0.82[CEU][hapmap];0.91[EUR][1000 genomes]
rs4671945	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs4671946	0.87[EUR][1000 genomes]
rs4671947	0.87[EUR][1000 genomes]
rs4671949	0.89[EUR][1000 genomes]
rs4671951	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs4671955	0.84[EUR][1000 genomes]
rs4671956	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs4671960	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs4671961	0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs4990319	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6545411	0.81[EUR][1000 genomes]
rs6545413	0.81[EUR][1000 genomes]
rs6545414	0.81[EUR][1000 genomes]
rs6545415	0.81[EUR][1000 genomes]
rs6545418	0.83[EUR][1000 genomes]
rs6545419	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs6545427	0.89[EUR][1000 genomes]
rs6545429	0.85[CEU][hapmap];0.91[EUR][1000 genomes]
rs6545434	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6704769	0.84[EUR][1000 genomes]
rs6706372	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6724590	0.84[EUR][1000 genomes]
rs6729826	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs6732949	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6734658	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6735813	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6742607	0.81[EUR][1000 genomes]
rs6746306	0.83[EUR][1000 genomes]
rs6748816	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6760298	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs6761369	0.86[CEU][hapmap];0.89[EUR][1000 genomes]
rs6761398	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs7558950	0.89[EUR][1000 genomes]
rs7563706	0.84[EUR][1000 genomes]
rs7589236	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs7607451	0.95[CEU][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs907135	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998277	chr2:54710337-54849648	Genic enhancers Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv961318	chr2:54818096-54823449	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54802200-54822600	Weak transcription	Esophagus	oesophagus
2	chr2:54804000-54822400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:54805400-54830200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:54807000-54826000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:54808800-54822800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:54809600-54825800	Weak transcription	Brain Germinal Matrix	brain
7	chr2:54814000-54822800	Weak transcription	Ovary	ovary
8	chr2:54815400-54823400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr2:54816200-54830600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:54816600-54822400	Weak transcription	Gastric	stomach
11	chr2:54816600-54822400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:54816600-54822600	Weak transcription	Colonic Mucosa	Colon
13	chr2:54816600-54828400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:54816800-54822400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:54816800-54822600	Weak transcription	Placenta	Placenta
16	chr2:54816800-54823000	Weak transcription	Aorta	Aorta
17	chr2:54816800-54823200	Weak transcription	Fetal Kidney	kidney
18	chr2:54816800-54823400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr2:54817000-54822400	Weak transcription	NHLF	lung
20	chr2:54817000-54822600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:54817000-54822800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:54817000-54823200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:54817000-54823200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr2:54817000-54825800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:54817000-54826200	Weak transcription	NHDF-Ad	bronchial
26	chr2:54817400-54822600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:54817400-54823000	Weak transcription	Dnd41	blood
28	chr2:54817400-54823200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:54817400-54823400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:54817400-54825400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:54817600-54822400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr2:54817600-54822600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:54817600-54822800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:54817600-54823600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:54817600-54825000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:54817600-54825600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:54817800-54822200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr2:54817800-54822400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:54817800-54822600	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:54817800-54822800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr2:54817800-54823000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr2:54817800-54823000	Weak transcription	NH-A	brain
43	chr2:54817800-54823400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:54817800-54825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:54817800-54826200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:54817800-54826200	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:54818000-54822200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:54818000-54822400	Weak transcription	Right Ventricle	heart
49	chr2:54818000-54824400	Weak transcription	HMEC	breast
50	chr2:54818000-54826200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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