Variant report

Variant	rs10030687
Chromosome Location	chr4:2938687-2938688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:199)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:199 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOSL1	chr4:2938602-2938860	K562	blood:	n/a	n/a
2	POLR2A	chr4:2936416-2939933	GM18505	blood:	n/a	n/a
3	POLR2A	chr4:2936463-2940004	GM12891	blood:	n/a	n/a
4	POLR2A	chr4:2938272-2939348	GM10847	blood:	n/a	n/a
5	POLR2A	chr4:2936427-2939614	Hela-S3	cervix:	n/a	n/a
6	TCF3	chr4:2938448-2938920	GM12878	blood:	n/a	n/a
7	FOS	chr4:2938583-2939331	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr4:2935540-2939822	Hela-S3	cervix:	n/a	n/a
9	MAX	chr4:2936301-2939648	HCT-116	colon:	n/a	n/a
10	RELA	chr4:2937153-2939870	GM18505	blood:	n/a	n/a
11	CHD2	chr4:2937878-2939510	GM12878	blood:	n/a	n/a
12	MTA3	chr4:2936419-2940060	GM12878	blood:	n/a	n/a
13	POLR2A	chr4:2936420-2939905	K562	blood:	n/a	n/a
14	POLR2A	chr4:2936475-2940008	GM12891	blood:	n/a	n/a
15	POLR2A	chr4:2937124-2940033	K562	blood:	n/a	n/a
16	SIN3AK20	chr4:2936414-2939621	HCT-116	colon:	n/a	n/a
17	POLR2A	chr4:2937075-2939631	H1-hESC	embryonic stem cell:	n/a	n/a
18	BCLAF1	chr4:2937706-2939670	GM12878	blood:	n/a	n/a
19	EBF1	chr4:2938521-2939453	GM12878	blood:	n/a	chr4:2939154-2939165
20	BCL11A	chr4:2938483-2939312	GM12878	blood:	n/a	n/a
21	NFATC1	chr4:2936959-2939864	GM12878	blood:	n/a	n/a
22	JUND	chr4:2937092-2939655	HCT-116	colon:	n/a	n/a
23	MYBL2	chr4:2938634-2939413	HepG2	liver:	n/a	n/a
24	POLR2A	chr4:2936428-2940062	K562	blood:	n/a	n/a
25	POLR2A	chr4:2936474-2938797	IMR90	lung:	n/a	n/a
26	POLR2A	chr4:2936942-2939390	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr4:2936392-2939634	HCT-116	colon:	n/a	n/a
28	POLR2A	chr4:2936273-2939674	MCF-7	breast:	n/a	n/a
29	BATF	chr4:2938406-2939380	GM12878	blood:	n/a	n/a
30	POLR2A	chr4:2938268-2939626	Raji	blood:	n/a	n/a
31	POLR2A	chr4:2938626-2938835	A549	lung:	n/a	n/a
32	STAT1	chr4:2938593-2939454	GM12878	blood:	n/a	n/a
33	POLR2A	chr4:2936425-2939503	HCT-116	colon:	n/a	n/a
34	POLR2A	chr4:2937759-2939502	K562	blood:	n/a	n/a
35	IRF4	chr4:2938488-2939713	GM12878	blood:	n/a	n/a
36	TBL1XR1	chr4:2937858-2939653	GM12878	blood:	n/a	n/a
37	POLR2A	chr4:2936447-2940060	GM12892	blood:	n/a	n/a
38	RELA	chr4:2936499-2938801	GM12891	blood:	n/a	n/a
39	TCF7L2	chr4:2938678-2939447	PANC-1	pancreas:	n/a	n/a
40	FOS	chr4:2938567-2939365	MCF10A-Er-Src	breast:	n/a	n/a
41	CHD2	chr4:2938417-2938727	K562	blood:	n/a	n/a
42	POLR2A	chr4:2938378-2939244	SK-N-SH	brain:	n/a	n/a
43	POLR2A	chr4:2938507-2939387	A549	lung:	n/a	n/a
44	POLR2A	chr4:2936481-2939398	PBDE	blood:	n/a	n/a
45	IKZF1	chr4:2937926-2939864	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:2936416-2940081	GM12878	blood:	n/a	n/a
47	ELF1	chr4:2938386-2939596	GM12878	blood:	n/a	n/a
48	MYC	chr4:2937183-2939811	MCF10A-Er-Src	breast:	n/a	n/a
49	TCF3	chr4:2938482-2938840	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:2937058-2939858	K562	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:2756410..2759745-chr4:2935120..2939466,6	K562	blood:
2	chr4:2830493..2833231-chr4:2936573..2940194,3	MCF-7	breast:
3	chr4:2888603..2889496-chr4:2938489..2939073,2	MCF-7	breast:
4	chr4:2903718..2915473-chr4:2930612..2941584,27	MCF-7	breast:
5	chr4:2793408..2795261-chr4:2937928..2940807,2	MCF-7	breast:
6	chr4:2795447..2803617-chr4:2934606..2939244,18	MCF-7	breast:
7	chr4:2818590..2823604-chr4:2934968..2940177,8	MCF-7	breast:
8	chr4:2790052..2809152-chr4:2930639..2948075,83	MCF-7	breast:
9	chr4:2744637..2750348-chr4:2934999..2939149,7	MCF-7	breast:
10	chr4:2756586..2759605-chr4:2935863..2938872,4	K562	blood:
11	chr4:2845404..2847784-chr4:2938194..2940916,3	MCF-7	breast:
12	chr4:2936565..2939326-chr4:2970679..2973500,2	K562	blood:
13	chr4:2842030..2853279-chr4:2934021..2940851,24	MCF-7	breast:
14	chr4:2867681..2870567-chr4:2936383..2939288,2	MCF-7	breast:
15	chr4:2799331..2801814-chr4:2936733..2939693,2	K562	blood:
16	chr4:2936328..2940860-chr4:2961848..2966602,8	K562	blood:
17	chr4:2753882..2759883-chr4:2932429..2941474,15	MCF-7	breast:
18	chr4:2906552..2911481-chr4:2934891..2942965,11	MCF-7	breast:
19	chr18:3447926..3450158-chr4:2936583..2939331,2	MCF-7	breast:
20	chr12:104680883..104682793-chr4:2937932..2939461,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ADD1-1	chr4:2937273-2939869	ENSG00000249673
2	lnc-ADD1-1	chr4:2937278-2939869	NR_015453

No data

Variant related genes	Relation type
MFSD10	TF binding region
NOP14-AS1	TF binding region
ENSG00000198431	Chromatin interaction
ENSG00000177426	Chromatin interaction
ENSG00000168884	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000125388	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000087266	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10026416	0.88[EUR][1000 genomes]
rs10031688	0.88[EUR][1000 genomes]
rs10050109	0.88[EUR][1000 genomes]
rs13111546	1.00[AFR][1000 genomes]
rs16843511	0.88[EUR][1000 genomes]
rs28510410	1.00[EUR][1000 genomes]
rs28707127	1.00[AFR][1000 genomes]
rs28747380	1.00[EUR][1000 genomes]
rs34209081	1.00[EUR][1000 genomes]
rs35640772	1.00[EUR][1000 genomes]
rs58168444	0.88[EUR][1000 genomes]
rs71608242	1.00[AFR][1000 genomes]
rs9991144	1.00[AFR][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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 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	chr4:2936600-2939600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr4:2936800-2939000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr4:2937000-2939000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:2937200-2938800	Flanking Active TSS	NH-A	brain
5	chr4:2937200-2939600	Flanking Active TSS	HMEC	breast
6	chr4:2937200-2939800	Transcr. at gene 5' and 3'	NHEK	skin
7	chr4:2937400-2939000	Flanking Active TSS	Hela-S3	cervix
8	chr4:2937400-2939400	Weak transcription	Ovary	ovary
9	chr4:2937600-2938800	Enhancers	Brain Substantia Nigra	brain
10	chr4:2937600-2939000	Enhancers	Primary B cells from peripheral blood	blood
11	chr4:2937600-2939000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr4:2937600-2939000	Genic enhancers	Fetal Stomach	stomach
13	chr4:2937600-2939000	Enhancers	Lung	lung
14	chr4:2937600-2939000	Enhancers	Pancreas	Pancrea
15	chr4:2937600-2939200	Enhancers	Liver	Liver
16	chr4:2937600-2939200	Enhancers	Fetal Heart	heart
17	chr4:2937600-2939200	Enhancers	Fetal Thymus	thymus
18	chr4:2937600-2939200	Genic enhancers	Stomach Smooth Muscle	stomach
19	chr4:2937600-2939200	Flanking Active TSS	GM12878-XiMat	blood
20	chr4:2937600-2939600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
21	chr4:2937600-2939600	Enhancers	Stomach Mucosa	stomach
22	chr4:2937800-2938800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:2937800-2938800	Weak transcription	Left Ventricle	heart
24	chr4:2937800-2939000	Weak transcription	Colonic Mucosa	Colon
25	chr4:2937800-2939200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:2937800-2939200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:2937800-2939200	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr4:2937800-2939400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr4:2937800-2939400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
30	chr4:2937800-2939400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:2937800-2939400	Genic enhancers	Fetal Muscle Trunk	muscle
32	chr4:2937800-2939400	Genic enhancers	Fetal Muscle Leg	muscle
33	chr4:2937800-2939400	Enhancers	Psoas Muscle	Psoas
34	chr4:2937800-2939400	Genic enhancers	NHLF	lung
35	chr4:2937800-2939600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:2937800-2939600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr4:2937800-2939600	Enhancers	NHDF-Ad	bronchial
38	chr4:2937800-2939800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:2937800-2940000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr4:2937800-2941800	Weak transcription	Small Intestine	intestine
41	chr4:2937800-2942400	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:2937800-2945800	Weak transcription	Fetal Kidney	kidney
43	chr4:2938000-2938800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:2938000-2938800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr4:2938000-2938800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:2938000-2938800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr4:2938000-2938800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr4:2938000-2938800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:2938000-2938800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr4:2938000-2938800	Weak transcription	Fetal Lung	lung

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