Variant report

Variant	rs16890177
Chromosome Location	chr6:37791101-37791102
allele	C/G
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	MYC	chr6:37790840-37791427	K562	blood:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
2	MYC	chr6:37790779-37791562	MCF10A-Er-Src	breast:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
3	GATA2	chr6:37790468-37791108	K562	blood:	n/a	n/a
4	CEBPD	chr6:37790427-37791195	K562	blood:	n/a	n/a
5	GATA1	chr6:37790447-37791191	PBDE	blood:	n/a	chr6:37791124-37791131
6	RCOR1	chr6:37790642-37791108	K562	blood:	n/a	n/a
7	MAX	chr6:37790791-37791528	K562	blood:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
8	CEBPD	chr6:37790397-37791132	K562	blood:	n/a	n/a
9	GATA1	chr6:37790217-37791654	K562	blood:	n/a	chr6:37791124-37791131
10	POLR2A	chr6:37790243-37791225	GM12878	blood:	n/a	n/a
11	POLR2A	chr6:37790777-37791396	GM12878	blood:	n/a	n/a
12	MYC	chr6:37790725-37791416	K562	blood:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
13	TEAD4	chr6:37790610-37791145	K562	blood:	n/a	n/a
14	TEAD4	chr6:37790564-37791126	K562	blood:	n/a	n/a
15	MYC	chr6:37790718-37791554	MCF10A-Er-Src	breast:	n/a	chr6:37791389-37791399 chr6:37791389-37791400 chr6:37791390-37791397 chr6:37791389-37791400 chr6:37791391-37791400 chr6:37791388-37791401 chr6:37791390-37791399
16	POLR2A	chr6:37790881-37791113	MCF10A-Er-Src	breast:	n/a	n/a
17	ZNF263	chr6:37790472-37791345	HEK293-T-REx	kidney:	n/a	n/a
18	FOS	chr6:37790780-37791113	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:37790138..37792445-chr6:37803004..37804688,2	MCF-7	breast:
2	chr6:37788598..37791926-chr6:37799655..37801709,3	K562	blood:
3	chr6:37790878..37792753-chr6:37808430..37810032,2	K562	blood:
4	chr6:37788608..37792008-chr6:37826692..37829268,3	K562	blood:
5	chr6:37785884..37787754-chr6:37789028..37791294,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225945	TF binding region
ENSG00000243313	Chromatin interaction
ENSG00000225945	Chromatin interaction
ENSG00000156639	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10485030	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs10498739	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10498740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10947702	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs10947704	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs11750950	0.95[CHB][hapmap];0.89[JPT][hapmap]
rs11751781	0.86[CHB][hapmap]
rs11751962	0.82[ASN][1000 genomes]
rs11752521	0.86[CHB][hapmap]
rs11752863	0.84[ASN][1000 genomes]
rs11755095	0.82[ASN][1000 genomes]
rs11755629	0.86[CHB][hapmap]
rs11756713	0.86[CHB][hapmap]
rs11757161	0.82[ASN][1000 genomes]
rs11759496	0.81[ASN][1000 genomes]
rs11759826	0.86[CHB][hapmap]
rs11967129	0.82[ASN][1000 genomes]
rs12660498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12660773	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes]
rs12660922	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12661109	1.00[AMR][1000 genomes]
rs12661378	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs12661480	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12661702	0.82[ASN][1000 genomes]
rs12662305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[ASN][1000 genomes]
rs12662426	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs12662823	1.00[AMR][1000 genomes]
rs12663957	1.00[AMR][1000 genomes]
rs12664091	0.85[CHB][hapmap]
rs12664768	0.86[CHB][hapmap]
rs13195545	0.82[ASN][1000 genomes]
rs13205311	0.82[ASN][1000 genomes]
rs13206035	0.85[CHB][hapmap]
rs16890168	0.87[JPT][hapmap]
rs16890175	0.90[CHB][hapmap];0.83[ASN][1000 genomes]
rs16890181	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16890215	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16890247	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs16890298	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16890299	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs16890301	0.90[CHB][hapmap]
rs16890305	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16890307	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs16890309	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs2025431	0.82[ASN][1000 genomes]
rs2064795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2273441	0.85[CHB][hapmap]
rs2274090	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2274091	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs2395689	0.90[CHB][hapmap]
rs2842510	0.85[CHB][hapmap]
rs2842511	0.90[CHB][hapmap]
rs2842521	0.85[CHB][hapmap]
rs35122358	0.82[ASN][1000 genomes]
rs35216205	0.82[ASN][1000 genomes]
rs3844314	0.86[CHB][hapmap]
rs3852216	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56093219	0.83[ASN][1000 genomes]
rs57198506	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs57276677	0.87[ASN][1000 genomes]
rs57402213	0.81[ASN][1000 genomes]
rs57458792	1.00[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs57911756	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs58084785	1.00[AMR][1000 genomes]
rs58320470	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs58473303	1.00[AMR][1000 genomes]
rs58692659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59036086	1.00[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59103990	1.00[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59649654	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59859268	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60141491	1.00[ASN][1000 genomes]
rs60284537	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60404082	1.00[AMR][1000 genomes]
rs60508820	1.00[AMR][1000 genomes]
rs60637081	1.00[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60883115	1.00[AMR][1000 genomes]
rs61090283	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61108907	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs61277916	1.00[AMR][1000 genomes]
rs61332486	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs61466900	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6458032	0.86[CHB][hapmap]
rs6906289	0.80[CHB][hapmap]
rs6911716	0.86[CHB][hapmap]
rs72849341	0.83[ASN][1000 genomes]
rs73421436	0.84[ASN][1000 genomes]
rs73421439	0.84[ASN][1000 genomes]
rs752110	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7739801	0.94[CHB][hapmap];1.00[YRI][hapmap]
rs7742226	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7746266	0.85[CHB][hapmap]
rs7748312	0.86[CHB][hapmap]
rs7756261	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs7759145	0.82[ASN][1000 genomes]
rs7759792	0.85[CHB][hapmap]
rs7761561	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs7764130	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7773419	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7775794	0.86[CHB][hapmap]

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	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1017051	chr6:37789341-38084719	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv538203	chr6:37789341-38084719	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37788600-37791400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr6:37788600-37791400	Enhancers	Small Intestine	intestine
3	chr6:37788800-37791400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:37788800-37791400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr6:37788800-37791400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:37788800-37791400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:37788800-37791400	Enhancers	Brain Substantia Nigra	brain
8	chr6:37788800-37791400	Enhancers	Placenta	Placenta
9	chr6:37788800-37791400	Enhancers	Fetal Stomach	stomach
10	chr6:37788800-37791600	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr6:37788800-37791800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr6:37788800-37792000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr6:37788800-37792000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr6:37789000-37791200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr6:37789000-37791400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr6:37789000-37791400	Enhancers	Brain Cingulate Gyrus	brain
17	chr6:37789000-37791400	Enhancers	Fetal Thymus	thymus
18	chr6:37789000-37791400	Enhancers	Ovary	ovary
19	chr6:37789000-37791400	Enhancers	Sigmoid Colon	Sigmoid Colon
20	chr6:37789000-37791600	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr6:37789000-37791600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:37789000-37791600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr6:37789000-37791800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:37789000-37791800	Enhancers	Left Ventricle	heart
25	chr6:37789000-37791800	Enhancers	Lung	lung
26	chr6:37789000-37791800	Enhancers	Right Atrium	heart
27	chr6:37789000-37792200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:37789000-37794400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:37789000-37796400	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr6:37789200-37791400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:37789200-37791400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:37789200-37791400	Enhancers	Gastric	stomach
33	chr6:37789200-37791400	Enhancers	Spleen	Spleen
34	chr6:37789200-37791600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:37789200-37791800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:37789400-37791200	Enhancers	H1 Cell Line	embryonic stem cell
37	chr6:37789400-37791200	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:37789400-37791200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:37789400-37791400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr6:37789400-37791400	Enhancers	Brain Anterior Caudate	brain
41	chr6:37789400-37791400	Enhancers	Pancreas	Pancrea
42	chr6:37789400-37791800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr6:37789400-37792400	Enhancers	Fetal Brain Male	brain
44	chr6:37789400-37800000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr6:37789600-37791200	Active TSS	GM12878-XiMat	blood
46	chr6:37789600-37791400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:37789600-37791400	Enhancers	Fetal Brain Female	brain
48	chr6:37789600-37791400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr6:37789600-37791600	Enhancers	Fetal Lung	lung
50	chr6:37789600-37792000	Enhancers	Fetal Muscle Trunk	muscle

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