Variant report

Variant	rs7921642
Chromosome Location	chr10:6338692-6338693
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr10:6338630-6339268	T-47D	breast:	n/a	n/a
2	NR2F2	chr10:6338586-6340495	MCF-7	breast:	n/a	n/a
3	STAT3	chr10:6338402-6338745	MCF10A-Er-Src	breast:	n/a	chr10:6338553-6338564
4	GATA3	chr10:6338503-6340513	MCF-7	breast:	n/a	chr10:6340157-6340165 chr10:6339062-6339070
5	SRF	chr10:6338433-6338736	K562	blood:	n/a	n/a
6	EP300	chr10:6338633-6339361	T-47D	breast:	n/a	n/a
7	ESR1	chr10:6338627-6339371	T-47D	breast:	n/a	n/a
8	ESR1	chr10:6338469-6339394	T-47D	breast:	n/a	n/a
9	POU2F2	chr10:6338403-6338910	GM12878	blood:	n/a	n/a
10	FOXM1	chr10:6338607-6340526	MCF-7	breast:	n/a	n/a
11	STAT5A	chr10:6338408-6338781	K562	blood:	n/a	n/a
12	JUND	chr10:6338625-6340488	T-47D	breast:	n/a	chr10:6339976-6339987
13	TCF12	chr10:6338592-6340561	MCF-7	breast:	n/a	n/a
14	FOXM1	chr10:6338596-6340427	MCF-7	breast:	n/a	n/a
15	STAT1	chr10:6338379-6338762	Hela-S3	cervix:	n/a	chr10:6338553-6338564 chr10:6338574-6338585
16	EP300	chr10:6338586-6340488	MCF-7	breast:	n/a	chr10:6339630-6339640
17	ESR1	chr10:6338540-6339345	T-47D	breast:	n/a	n/a
18	ESR1	chr10:6338510-6339351	T-47D	breast:	n/a	n/a
19	POLR2A	chr10:6338326-6339120	GM12878	blood:	n/a	n/a
20	IRF1	chr10:6338472-6338693	K562	blood:	n/a	n/a
21	GATA3	chr10:6338621-6340547	MCF-7	breast:	n/a	chr10:6340157-6340165 chr10:6339062-6339070
22	STAT5A	chr10:6338278-6338872	K562	blood:	n/a	n/a
23	SIN3AK20	chr10:6338590-6340604	MCF-7	breast:	n/a	n/a
24	ESR1	chr10:6338532-6339359	T-47D	breast:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:6337874..6340921-chr10:6402269..6405461,3	MCF-7	breast:
2	chr10:6310906..6315323-chr10:6338181..6341379,4	MCF-7	breast:
3	chr10:6337684..6340444-chr2:11681224..11683590,2	MCF-7	breast:
4	chr10:6240895..6249179-chr10:6337425..6345825,48	MCF-7	breast:
5	chr10:6338315..6339996-chr10:6419435..6421354,2	MCF-7	breast:
6	chr10:6317151..6318680-chr10:6338144..6339760,2	MCF-7	breast:
7	chr10:6242967..6247217-chr10:6336875..6343685,22	MCF-7	breast:
8	chr10:6256425..6258946-chr10:6338199..6341080,3	MCF-7	breast:
9	chr10:6338687..6345306-chr10:6353335..6358938,10	MCF-7	breast:
10	chr10:6255825..6258617-chr10:6338081..6340020,2	MCF-7	breast:
11	chr10:6337812..6339810-chr10:6355457..6358374,2	MCF-7	breast:
12	chr10:6335862..6338151-chr10:6338525..6340417,2	K562	blood:
13	chr10:6333704..6336118-chr10:6337786..6340640,2	MCF-7	breast:
14	chr10:6337823..6339767-chr10:6360899..6362837,2	MCF-7	breast:
15	chr10:6332709..6335479-chr10:6337457..6338999,2	MCF-7	breast:
16	chr10:6316454..6323166-chr10:6337458..6343783,14	MCF-7	breast:
17	chr10:6185488..6188042-chr10:6337910..6339714,2	MCF-7	breast:
18	chr10:6336971..6341697-chr10:6441247..6445868,11	MCF-7	breast:
19	chr10:6337574..6341267-chr10:6434955..6438365,4	MCF-7	breast:
20	chr10:6338433..6344348-chr10:6402915..6408706,10	MCF-7	breast:
21	chr10:6319975..6324028-chr10:6337597..6341506,5	MCF-7	breast:
22	chr10:6296201..6297782-chr10:6337889..6339663,2	MCF-7	breast:

No data

Variant related genes	Relation type
SDCBPP1	TF binding region
ENSG00000170525	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000213994	Chromatin interaction
ENSG00000226705	Chromatin interaction
ENSG00000215244	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10906207	0.88[ASN][1000 genomes]
rs11257854	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12259346	0.90[ASN][1000 genomes]
rs4403713	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4420170	0.86[ASN][1000 genomes]
rs4747994	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6602609	0.86[ASN][1000 genomes]
rs7088356	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7896262	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7906792	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7918684	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][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	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6322600-6339000	Weak transcription	Esophagus	oesophagus
2	chr10:6332800-6338800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:6333000-6341800	Weak transcription	NHDF-Ad	bronchial
4	chr10:6333400-6338800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr10:6333400-6341000	Weak transcription	Thymus	Thymus
6	chr10:6333600-6338800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr10:6333600-6339000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr10:6333600-6339000	Weak transcription	Adipose Nuclei	Adipose
9	chr10:6333800-6338800	Weak transcription	Stomach Mucosa	stomach
10	chr10:6333800-6339000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:6333800-6339000	Weak transcription	Brain Anterior Caudate	brain
12	chr10:6333800-6339000	Weak transcription	Fetal Lung	lung
13	chr10:6333800-6339000	Weak transcription	HepG2	liver
14	chr10:6333800-6339200	Weak transcription	Fetal Intestine Large	intestine
15	chr10:6333800-6339800	Weak transcription	Brain Substantia Nigra	brain
16	chr10:6333800-6341800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr10:6334000-6341000	Weak transcription	Dnd41	blood
18	chr10:6334000-6341600	Weak transcription	Primary T cells from cord blood	blood
19	chr10:6334000-6341600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr10:6334200-6339000	Weak transcription	Right Atrium	heart
21	chr10:6334200-6341200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr10:6334200-6341600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr10:6334600-6341600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr10:6334600-6341600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr10:6335200-6338800	Weak transcription	Hela-S3	cervix
26	chr10:6335200-6339000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr10:6335200-6339800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr10:6335400-6339000	Weak transcription	Fetal Kidney	kidney
29	chr10:6335600-6339800	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr10:6335800-6339000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr10:6336000-6339400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr10:6336600-6339600	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr10:6337000-6339600	Enhancers	GM12878-XiMat	blood
34	chr10:6337600-6339000	Enhancers	A549	lung
35	chr10:6337600-6341200	Enhancers	Placenta Amnion	Placenta Amnion
36	chr10:6337800-6339400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr10:6337800-6340400	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr10:6337800-6341200	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr10:6338000-6339000	Weak transcription	Placenta	Placenta
40	chr10:6338000-6339000	Weak transcription	Spleen	Spleen
41	chr10:6338000-6339600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr10:6338000-6341200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr10:6338200-6342200	Enhancers	Duodenum Mucosa	Duodenum
44	chr10:6338400-6339600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr10:6338400-6339600	Weak transcription	Primary B cells from cord blood	blood
46	chr10:6338400-6339600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr10:6338400-6339800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:6338400-6339800	Enhancers	Small Intestine	intestine
49	chr10:6338400-6344000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr10:6338600-6339400	Enhancers	Left Ventricle	heart

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