Variant report

Variant	rs6602601
Chromosome Location	chr10:6339240-6339241
allele	A/C
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	SIN3AK20	chr10:6338782-6340413	MCF-7	breast:	n/a	n/a
2	ESR1	chr10:6338630-6339268	T-47D	breast:	n/a	n/a
3	EP300	chr10:6338846-6340490	A549	lung:	n/a	chr10:6339630-6339640
4	NR2F2	chr10:6338586-6340495	MCF-7	breast:	n/a	n/a
5	GATA3	chr10:6338503-6340513	MCF-7	breast:	n/a	chr10:6340157-6340165 chr10:6339062-6339070
6	ELF1	chr10:6338850-6339271	A549	lung:	n/a	chr10:6339077-6339088 chr10:6339075-6339088 chr10:6339182-6339194
7	EP300	chr10:6338633-6339361	T-47D	breast:	n/a	n/a
8	FOXA1	chr10:6338856-6339308	T-47D	breast:	n/a	n/a
9	SP1	chr10:6338806-6340645	A549	lung:	n/a	chr10:6340030-6340044
10	GATA3	chr10:6338829-6340349	MCF-7	breast:	n/a	chr10:6340157-6340165 chr10:6339062-6339070
11	ESR1	chr10:6338627-6339371	T-47D	breast:	n/a	n/a
12	TCF12	chr10:6338736-6340489	MCF-7	breast:	n/a	n/a
13	MAX	chr10:6338757-6340407	MCF-7	breast:	n/a	n/a
14	ELF1	chr10:6338800-6339317	A549	lung:	n/a	chr10:6339077-6339088 chr10:6339075-6339088 chr10:6339182-6339194
15	ESR1	chr10:6338469-6339394	T-47D	breast:	n/a	n/a
16	NR3C1	chr10:6338961-6340462	A549	lung:	n/a	chr10:6339561-6339575 chr10:6339980-6339998 chr10:6340017-6340024
17	FOXM1	chr10:6338607-6340526	MCF-7	breast:	n/a	n/a
18	EP300	chr10:6338796-6342469	A549	lung:	n/a	chr10:6340963-6340977 chr10:6341190-6341200 chr10:6339630-6339640
19	JUND	chr10:6338625-6340488	T-47D	breast:	n/a	chr10:6339976-6339987
20	TCF12	chr10:6338592-6340561	MCF-7	breast:	n/a	n/a
21	GATA3	chr10:6338727-6339358	T-47D	breast:	n/a	chr10:6339062-6339070
22	SP1	chr10:6338808-6340604	A549	lung:	n/a	chr10:6340030-6340044
23	FOXM1	chr10:6338596-6340427	MCF-7	breast:	n/a	n/a
24	ZNF217	chr10:6338925-6340543	MCF-7	breast:	n/a	n/a
25	MAX	chr10:6338802-6340497	A549	lung:	n/a	n/a
26	ELF1	chr10:6338713-6340466	MCF-7	breast:	n/a	chr10:6339077-6339088 chr10:6339075-6339088 chr10:6339182-6339194
27	BCL3	chr10:6339131-6340380	A549	lung:	n/a	chr10:6339671-6339679
28	GATA3	chr10:6339170-6340748	A549	lung:	n/a	chr10:6340157-6340165
29	ELF1	chr10:6338749-6339492	HCT-116	colon:	n/a	chr10:6339077-6339088 chr10:6339075-6339088 chr10:6339182-6339194
30	EP300	chr10:6338586-6340488	MCF-7	breast:	n/a	chr10:6339630-6339640
31	ESR1	chr10:6338540-6339345	T-47D	breast:	n/a	n/a
32	NR2F2	chr10:6338718-6340496	MCF-7	breast:	n/a	n/a
33	FOXA1	chr10:6338880-6339281	T-47D	breast:	n/a	n/a
34	ESR1	chr10:6338510-6339351	T-47D	breast:	n/a	n/a
35	WRNIP1	chr10:6339209-6339351	GM12878	blood:	n/a	n/a
36	ELF1	chr10:6338759-6340416	MCF-7	breast:	n/a	chr10:6339077-6339088 chr10:6339075-6339088 chr10:6339182-6339194
37	ELF1	chr10:6338842-6339284	K562	blood:	n/a	chr10:6339077-6339088 chr10:6339075-6339088 chr10:6339182-6339194
38	GATA3	chr10:6338699-6340447	T-47D	breast:	n/a	chr10:6340157-6340165 chr10:6339062-6339070
39	EP300	chr10:6338730-6339350	T-47D	breast:	n/a	n/a
40	GATA3	chr10:6338621-6340547	MCF-7	breast:	n/a	chr10:6340157-6340165 chr10:6339062-6339070
41	TCF12	chr10:6338726-6342939	A549	lung:	n/a	n/a
42	SIN3AK20	chr10:6338590-6340604	MCF-7	breast:	n/a	n/a
43	REST	chr10:6338918-6340657	A549	lung:	n/a	chr10:6339672-6339680
44	ESR1	chr10:6338532-6339359	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:6204469..6207295-chr10:6338789..6342054,3	MCF-7	breast:
2	chr10:6337874..6340921-chr10:6402269..6405461,3	MCF-7	breast:
3	chr10:6310906..6315323-chr10:6338181..6341379,4	MCF-7	breast:
4	chr10:6337684..6340444-chr2:11681224..11683590,2	MCF-7	breast:
5	chr10:6240895..6249179-chr10:6337425..6345825,48	MCF-7	breast:
6	chr10:6338315..6339996-chr10:6419435..6421354,2	MCF-7	breast:
7	chr10:6317151..6318680-chr10:6338144..6339760,2	MCF-7	breast:
8	chr10:6242967..6247217-chr10:6336875..6343685,22	MCF-7	breast:
9	chr10:6256425..6258946-chr10:6338199..6341080,3	MCF-7	breast:
10	chr10:6338687..6345306-chr10:6353335..6358938,10	MCF-7	breast:
11	chr10:6255825..6258617-chr10:6338081..6340020,2	MCF-7	breast:
12	chr10:6337812..6339810-chr10:6355457..6358374,2	MCF-7	breast:
13	chr10:6335862..6338151-chr10:6338525..6340417,2	K562	blood:
14	chr10:6333704..6336118-chr10:6337786..6340640,2	MCF-7	breast:
15	chr10:6337823..6339767-chr10:6360899..6362837,2	MCF-7	breast:
16	chr10:6306983..6309812-chr10:6338962..6341584,2	MCF-7	breast:
17	chr10:6316454..6323166-chr10:6337458..6343783,14	MCF-7	breast:
18	chr10:6185488..6188042-chr10:6337910..6339714,2	MCF-7	breast:
19	chr10:6279091..6282826-chr10:6339063..6342558,5	MCF-7	breast:
20	chr10:6336971..6341697-chr10:6441247..6445868,11	MCF-7	breast:
21	chr10:6337574..6341267-chr10:6434955..6438365,4	MCF-7	breast:
22	chr10:6338433..6344348-chr10:6402915..6408706,10	MCF-7	breast:
23	chr10:6319975..6324028-chr10:6337597..6341506,5	MCF-7	breast:
24	chr10:6296201..6297782-chr10:6337889..6339663,2	MCF-7	breast:

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

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

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

rs_ID	r²[population]
rs12251926	1.00[MEX][hapmap]
rs56719282	1.00[EUR][1000 genomes]
rs56804401	1.00[EUR][1000 genomes]
rs57027903	1.00[EUR][1000 genomes]
rs57388231	1.00[EUR][1000 genomes]
rs57572880	1.00[EUR][1000 genomes]
rs58167910	1.00[EUR][1000 genomes]
rs60201304	1.00[EUR][1000 genomes]
rs61621320	1.00[EUR][1000 genomes]
rs7083971	1.00[MEX][hapmap]
rs7896447	1.00[MEX][hapmap]

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:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6333000-6341800	Weak transcription	NHDF-Ad	bronchial
2	chr10:6333400-6341000	Weak transcription	Thymus	Thymus
3	chr10:6333800-6339800	Weak transcription	Brain Substantia Nigra	brain
4	chr10:6333800-6341800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr10:6334000-6341000	Weak transcription	Dnd41	blood
6	chr10:6334000-6341600	Weak transcription	Primary T cells from cord blood	blood
7	chr10:6334000-6341600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr10:6334200-6341200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr10:6334200-6341600	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr10:6334600-6341600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr10:6334600-6341600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr10:6335200-6339800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr10:6335600-6339800	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr10:6336000-6339400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr10:6336600-6339600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr10:6337000-6339600	Enhancers	GM12878-XiMat	blood
17	chr10:6337600-6341200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr10:6337800-6339400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr10:6337800-6340400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr10:6337800-6341200	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr10:6338000-6339600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:6338000-6341200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr10:6338200-6342200	Enhancers	Duodenum Mucosa	Duodenum
24	chr10:6338400-6339600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr10:6338400-6339600	Weak transcription	Primary B cells from cord blood	blood
26	chr10:6338400-6339600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr10:6338400-6339800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr10:6338400-6339800	Enhancers	Small Intestine	intestine
29	chr10:6338400-6344000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr10:6338600-6339400	Enhancers	Left Ventricle	heart
31	chr10:6338600-6339800	Enhancers	Fetal Thymus	thymus
32	chr10:6338600-6340800	Enhancers	NHEK	skin
33	chr10:6338600-6343000	Enhancers	HMEC	breast
34	chr10:6338600-6343800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:6338800-6339400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr10:6338800-6339600	Enhancers	Gastric	stomach
37	chr10:6338800-6339800	Enhancers	Pancreas	Pancrea
38	chr10:6338800-6340200	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr10:6338800-6340400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr10:6338800-6341000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr10:6338800-6342200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:6338800-6342200	Enhancers	Hela-S3	cervix
43	chr10:6338800-6342800	Enhancers	Aorta	Aorta
44	chr10:6338800-6343800	Enhancers	Stomach Mucosa	stomach
45	chr10:6338800-6345000	Enhancers	Fetal Intestine Small	intestine
46	chr10:6339000-6339400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr10:6339000-6339400	Enhancers	Colonic Mucosa	Colon
48	chr10:6339000-6339400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr10:6339000-6339400	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr10:6339000-6339400	Enhancers	Spleen	Spleen

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