Variant report

Variant	rs4838404
Chromosome Location	chr10:49495886-49495887
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr10:49495867-49496376	T-47D	breast:	n/a	n/a
2	MAX	chr10:49495811-49496811	MCF-7	breast:	n/a	chr10:49496389-49496399
3	EP300	chr10:49495792-49496505	MCF-7	breast:	n/a	n/a
4	CHD2	chr10:49495787-49496474	GM12878	blood:	n/a	n/a
5	NR2F2	chr10:49495675-49496849	MCF-7	breast:	n/a	n/a
6	GATA3	chr10:49495878-49496428	T-47D	breast:	n/a	n/a
7	FOXM1	chr10:49495874-49496477	MCF-7	breast:	n/a	n/a
8	FOXA1	chr10:49495744-49496269	T-47D	breast:	n/a	n/a
9	TCF12	chr10:49495792-49496512	MCF-7	breast:	n/a	n/a
10	GATA3	chr10:49495876-49496398	T-47D	breast:	n/a	n/a
11	POLR2A	chr10:49495664-49496232	GM12878	blood:	n/a	n/a
12	EBF1	chr10:49495884-49496476	GM12878	blood:	n/a	n/a
13	SIN3AK20	chr10:49495876-49496543	MCF-7	breast:	n/a	n/a
14	ESR1	chr10:49495867-49496352	T-47D	breast:	n/a	n/a
15	EP300	chr10:49495768-49496576	MCF-7	breast:	n/a	n/a
16	HA-E2F1	chr10:49495587-49496603	MCF-7	breast:	n/a	chr10:49495799-49495808
17	EBF1	chr10:49495883-49496497	GM12878	blood:	n/a	n/a
18	SIN3AK20	chr10:49495655-49496753	MCF-7	breast:	n/a	n/a
19	ELF1	chr10:49495620-49496728	MCF-7	breast:	n/a	n/a
20	PAX5	chr10:49495859-49496585	GM12878	blood:	n/a	n/a
21	NR2F2	chr10:49495743-49496514	MCF-7	breast:	n/a	n/a
22	POLR2A	chr10:49495409-49497069	GM12878	blood:	n/a	n/a
23	HDAC2	chr10:49495838-49496510	MCF-7	breast:	n/a	chr10:49496170-49496178
24	STAT1	chr10:49495724-49495896	GM12878	blood:	n/a	n/a
25	GATA3	chr10:49495679-49496750	MCF-7	breast:	n/a	n/a
26	HDAC2	chr10:49495824-49496572	MCF-7	breast:	n/a	chr10:49496170-49496178
27	FOXA1	chr10:49495691-49496204	T-47D	breast:	n/a	n/a
28	GATA3	chr10:49495741-49496883	MCF-7	breast:	n/a	n/a
29	TCF12	chr10:49495849-49496686	MCF-7	breast:	n/a	n/a
30	TBP	chr10:49495842-49496295	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:49495690..49496196-chr10:51547486..51547990,2	MCF-7	breast:
2	chr10:49494826..49497610-chr10:49513560..49515926,2	MCF-7	breast:
3	chr10:49422440..49425186-chr10:49494550..49500073,5	MCF-7	breast:
4	chr10:49495793..49496380-chr10:49514095..49514687,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225482	TF binding region
ENSG00000107643	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10745265	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs10776590	0.91[ASN][1000 genomes]
rs10776591	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10776592	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10776594	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs10857554	0.80[CEU][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10857564	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs10857565	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs11101280	0.91[ASN][1000 genomes]
rs11101281	0.90[ASN][1000 genomes]
rs11101282	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11101285	0.81[GIH][hapmap];0.88[JPT][hapmap]
rs1112268	0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs11597435	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs11598320	0.81[JPT][hapmap]
rs12358297	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs17780725	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs1881735	0.81[CHD][hapmap];0.88[JPT][hapmap]
rs1881737	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs1881740	0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs1881741	0.87[CHB][hapmap];0.84[JPT][hapmap]
rs1919706	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs1919707	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs1919709	0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs1919710	0.91[ASN][1000 genomes]
rs1997365	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs2377142	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2377143	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2377349	0.89[CHB][hapmap];0.81[CHD][hapmap];0.88[JPT][hapmap]
rs2590386	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs2590391	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs2698758	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2698768	0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2889595	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs4529852	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537559	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap]
rs7068398	0.82[JPT][hapmap]
rs7095392	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7097975	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs7898026	0.94[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.83[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	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv895368	chr10:49381635-49551560	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv550812	chr10:49484698-49524715	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4838404	ALG1L	trans	cerebellum	SCAN
rs4838404	ANTXRL	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49492400-49498200	Enhancers	Fetal Thymus	thymus
2	chr10:49493200-49499800	Enhancers	GM12878-XiMat	blood
3	chr10:49493600-49504200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:49494000-49497600	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr10:49494400-49498000	Weak transcription	Adipose Nuclei	Adipose
6	chr10:49494600-49496800	Flanking Active TSS	Dnd41	blood
7	chr10:49495000-49496400	Enhancers	Brain Germinal Matrix	brain
8	chr10:49495000-49498000	Enhancers	Brain Hippocampus Middle	brain
9	chr10:49495200-49496800	Enhancers	Brain Angular Gyrus	brain
10	chr10:49495200-49497800	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr10:49495200-49498200	Enhancers	Brain Substantia Nigra	brain
12	chr10:49495400-49496400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr10:49495400-49496600	Enhancers	Colon Smooth Muscle	Colon
14	chr10:49495400-49496600	Enhancers	Lung	lung
15	chr10:49495400-49496600	Enhancers	Right Ventricle	heart
16	chr10:49495400-49497000	Enhancers	Fetal Stomach	stomach
17	chr10:49495400-49497200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr10:49495400-49497200	Enhancers	Pancreas	Pancrea
19	chr10:49495400-49497400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:49495400-49497800	Enhancers	Brain Cingulate Gyrus	brain
21	chr10:49495400-49498200	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr10:49495400-49498800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr10:49495400-49500400	Enhancers	Placenta	Placenta
24	chr10:49495600-49496000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr10:49495600-49496200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr10:49495600-49496200	Enhancers	Fetal Muscle Leg	muscle
27	chr10:49495600-49496400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:49495600-49496400	Enhancers	Fetal Heart	heart
29	chr10:49495600-49496400	Enhancers	Right Atrium	heart
30	chr10:49495600-49496400	Enhancers	Stomach Smooth Muscle	stomach
31	chr10:49495600-49496600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr10:49495600-49496600	Enhancers	Rectal Smooth Muscle	rectum
33	chr10:49495600-49497000	Enhancers	Esophagus	oesophagus
34	chr10:49495600-49497800	Enhancers	Fetal Lung	lung
35	chr10:49495600-49498200	Enhancers	Brain Anterior Caudate	brain
36	chr10:49495600-49498800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr10:49495800-49496200	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr10:49495800-49496200	Enhancers	Fetal Brain Male	brain
39	chr10:49495800-49496200	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr10:49495800-49496200	Bivalent Enhancer	Stomach Mucosa	stomach
41	chr10:49495800-49496400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr10:49495800-49496400	Enhancers	Fetal Intestine Large	intestine
43	chr10:49495800-49496400	Enhancers	Gastric	stomach
44	chr10:49495800-49496400	Enhancers	NHEK	skin
45	chr10:49495800-49496600	Enhancers	Left Ventricle	heart
46	chr10:49495800-49496600	Enhancers	HMEC	breast
47	chr10:49495800-49497200	Enhancers	Primary hematopoietic stem cells short term culture	blood
48	chr10:49495800-49497800	Enhancers	Fetal Muscle Trunk	muscle
49	chr10:49495800-49498200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:49495800-49500400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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