Variant report

Variant	rs3778216
Chromosome Location	chr6:114280563-114280564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr6:114280336-114280827	K562	blood:	n/a	n/a
2	GATA1	chr6:114280090-114281007	PBDE	blood:	n/a	chr6:114280608-114280617 chr6:114280341-114280354
3	TEAD4	chr6:114280367-114280724	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:114279778..114281819-chr6:114290954..114293295,2	MCF-7	breast:

Variant related genes	Relation type
HDAC2	TF binding region
ENSG00000196591	Chromatin interaction
ENSG00000228624	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12660414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12660832	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665655	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13191525	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13191982	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13194921	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13201727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13204434	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]
rs13204445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13206211	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13208986	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13209064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212298	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13213007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213042	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13216873	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13219947	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1322453	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358945	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17075712	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2025191	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34319597	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34789089	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35846930	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs548388	0.90[CHB][hapmap];0.95[JPT][hapmap]

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	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

No data

Chromatin state (count:120 , 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	chr6:114254600-114281800	Strong transcription	Dnd41	blood
4	chr6:114255400-114281600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:114258600-114282600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:114258600-114291000	Weak transcription	Lung	lung
7	chr6:114258800-114281000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:114258800-114281600	Weak transcription	Gastric	stomach
9	chr6:114258800-114285600	Weak transcription	Right Ventricle	heart
10	chr6:114258800-114289800	Weak transcription	Spleen	Spleen
11	chr6:114259000-114289200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:114259400-114281400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr6:114259600-114281000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr6:114259800-114280600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:114259800-114280600	Strong transcription	Fetal Thymus	thymus
16	chr6:114259800-114280800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr6:114259800-114280800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr6:114259800-114281000	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr6:114264800-114289800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:114265200-114280800	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:114265600-114282000	Weak transcription	Brain Substantia Nigra	brain
22	chr6:114266000-114283800	Weak transcription	Colonic Mucosa	Colon
23	chr6:114266000-114289600	Weak transcription	Esophagus	oesophagus
24	chr6:114266200-114285600	Weak transcription	Psoas Muscle	Psoas
25	chr6:114266400-114285600	Weak transcription	Small Intestine	intestine
26	chr6:114266400-114289800	Weak transcription	Pancreas	Pancrea
27	chr6:114267400-114281400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr6:114267400-114281600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr6:114267400-114282200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr6:114267400-114286200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr6:114267400-114287200	Weak transcription	Fetal Brain Male	brain
32	chr6:114267400-114288800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr6:114267400-114289000	Weak transcription	Brain Angular Gyrus	brain
34	chr6:114267400-114289200	Weak transcription	Ovary	ovary
35	chr6:114267400-114289800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr6:114268000-114280600	Strong transcription	Primary B cells from cord blood	blood
37	chr6:114268200-114280800	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr6:114270400-114289800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr6:114272800-114281400	Weak transcription	Colon Smooth Muscle	Colon
40	chr6:114273600-114289200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr6:114275400-114280600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:114275400-114289200	Weak transcription	Left Ventricle	heart
43	chr6:114275600-114280600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr6:114275600-114280600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr6:114275800-114281000	Strong transcription	HSMM	muscle
46	chr6:114275800-114282800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr6:114275800-114286000	Weak transcription	Primary T cells from cord blood	blood
48	chr6:114276000-114280600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr6:114276000-114280600	Strong transcription	NH-A	brain
50	chr6:114276000-114289200	Weak transcription	A549	lung

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