Variant report

Variant	rs2499618
Chromosome Location	chr6:114285253-114285254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:114273569..114275934-chr6:114283284..114285737,2	K562	blood:
2	chr6:114277709..114279245-chr6:114283228..114285269,2	MCF-7	breast:
3	chr6:114281941..114287220-chr6:114288215..114294270,10	MCF-7	breast:
4	chr6:114178671..114180639-chr6:114284210..114286994,2	MCF-7	breast:
5	chr6:114270741..114273479-chr6:114282715..114285279,2	K562	blood:

Variant related genes	Relation type
ENSG00000228624	Chromatin interaction
ENSG00000196591	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs13203445	0.84[ASN][1000 genomes]
rs1407459	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2243356	0.82[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2475631	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2998738	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs352062	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352063	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352066	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352067	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352093	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3757016	0.92[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs471759	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs498519	0.84[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs499349	0.83[JPT][hapmap]
rs5027730	0.84[ASN][1000 genomes]
rs509827	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs515027	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs515049	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs530433	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs530459	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs534163	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs534169	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs541691	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs541824	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs543139	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs546087	0.84[JPT][hapmap]
rs549348	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs562296	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs576924	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577206	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs577474	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577580	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs580305	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs580425	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6568820	0.83[ASN][1000 genomes]
rs6917804	0.84[ASN][1000 genomes]
rs7754939	0.82[ASN][1000 genomes]
rs9398369	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv1021774	chr6:114063971-114407280	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv538422	chr6:114063971-114407280	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3363275	chr6:114101331-114302866	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	nsv520419	chr6:114285253-114306614	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:114253000-114289800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:114253400-114290600	Weak transcription	Aorta	Aorta
3	chr6:114258600-114291000	Weak transcription	Lung	lung
4	chr6:114258800-114285600	Weak transcription	Right Ventricle	heart
5	chr6:114258800-114289800	Weak transcription	Spleen	Spleen
6	chr6:114259000-114289200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:114264800-114289800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr6:114266000-114289600	Weak transcription	Esophagus	oesophagus
9	chr6:114266200-114285600	Weak transcription	Psoas Muscle	Psoas
10	chr6:114266400-114285600	Weak transcription	Small Intestine	intestine
11	chr6:114266400-114289800	Weak transcription	Pancreas	Pancrea
12	chr6:114267400-114286200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr6:114267400-114287200	Weak transcription	Fetal Brain Male	brain
14	chr6:114267400-114288800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:114267400-114289000	Weak transcription	Brain Angular Gyrus	brain
16	chr6:114267400-114289200	Weak transcription	Ovary	ovary
17	chr6:114267400-114289800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr6:114270400-114289800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:114273600-114289200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:114275400-114289200	Weak transcription	Left Ventricle	heart
21	chr6:114275800-114286000	Weak transcription	Primary T cells from cord blood	blood
22	chr6:114276000-114289200	Weak transcription	A549	lung
23	chr6:114276000-114289200	Weak transcription	HMEC	breast
24	chr6:114276000-114289400	Weak transcription	NHEK	skin
25	chr6:114276000-114289800	Weak transcription	NHLF	lung
26	chr6:114276800-114289000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr6:114277000-114288400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:114277000-114288600	Weak transcription	Fetal Intestine Small	intestine
29	chr6:114277000-114289200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:114277000-114289200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr6:114277000-114289400	Weak transcription	Fetal Stomach	stomach
32	chr6:114277000-114289800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:114277200-114289000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr6:114277200-114289200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:114277400-114288800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr6:114277400-114288800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr6:114277400-114289600	Weak transcription	Thymus	Thymus
38	chr6:114277400-114290200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr6:114277600-114289800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:114277800-114289800	Weak transcription	HSMMtube	muscle
41	chr6:114278000-114289200	Weak transcription	Liver	Liver
42	chr6:114278200-114288200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr6:114278600-114288200	Weak transcription	Fetal Kidney	kidney
44	chr6:114278600-114289800	Weak transcription	Placenta	Placenta
45	chr6:114278800-114289800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr6:114279000-114289200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:114279000-114289800	Weak transcription	Brain Anterior Caudate	brain
48	chr6:114279400-114289200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:114279400-114289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr6:114279600-114288600	Weak transcription	H1 Cell Line	embryonic stem cell

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