Variant report

Variant	rs7097975
Chromosome Location	chr10:49496417-49496418
allele	C/T
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	MAX	chr10:49495811-49496811	MCF-7	breast:	n/a	chr10:49496389-49496399
2	GATA3	chr10:49495994-49496546	MCF-7	breast:	n/a	n/a
3	RUNX3	chr10:49495927-49496531	GM12878	blood:	n/a	n/a
4	EP300	chr10:49495792-49496505	MCF-7	breast:	n/a	n/a
5	CHD2	chr10:49495787-49496474	GM12878	blood:	n/a	n/a
6	NR2F2	chr10:49495675-49496849	MCF-7	breast:	n/a	n/a
7	GATA3	chr10:49495878-49496428	T-47D	breast:	n/a	n/a
8	FOXM1	chr10:49495874-49496477	MCF-7	breast:	n/a	n/a
9	MAZ	chr10:49496068-49496513	GM12878	blood:	n/a	chr10:49496389-49496399
10	TCF12	chr10:49495792-49496512	MCF-7	breast:	n/a	n/a
11	RUNX3	chr10:49496056-49496459	GM12878	blood:	n/a	n/a
12	EBF1	chr10:49495884-49496476	GM12878	blood:	n/a	n/a
13	MXI1	chr10:49496062-49496472	GM12878	blood:	n/a	n/a
14	EBF1	chr10:49495904-49496497	GM12878	blood:	n/a	n/a
15	SIN3AK20	chr10:49495876-49496543	MCF-7	breast:	n/a	n/a
16	EP300	chr10:49495768-49496576	MCF-7	breast:	n/a	n/a
17	HA-E2F1	chr10:49495587-49496603	MCF-7	breast:	n/a	chr10:49495799-49495808
18	EBF1	chr10:49495883-49496497	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr10:49495655-49496753	MCF-7	breast:	n/a	n/a
20	CUX1	chr10:49496032-49496464	GM12878	blood:	n/a	n/a
21	ELF1	chr10:49495620-49496728	MCF-7	breast:	n/a	n/a
22	PAX5	chr10:49495859-49496585	GM12878	blood:	n/a	n/a
23	NR2F2	chr10:49495743-49496514	MCF-7	breast:	n/a	n/a
24	POLR2A	chr10:49495409-49497069	GM12878	blood:	n/a	n/a
25	HDAC2	chr10:49495838-49496510	MCF-7	breast:	n/a	chr10:49496170-49496178
26	GATA3	chr10:49495679-49496750	MCF-7	breast:	n/a	n/a
27	ZEB1	chr10:49496219-49496567	GM12878	blood:	n/a	n/a
28	HDAC2	chr10:49495824-49496572	MCF-7	breast:	n/a	chr10:49496170-49496178
29	ELK1	chr10:49496252-49496477	GM12878	blood:	n/a	n/a
30	GATA3	chr10:49495741-49496883	MCF-7	breast:	n/a	n/a
31	TCF12	chr10:49495849-49496686	MCF-7	breast:	n/a	n/a
32	EP300	chr10:49496054-49496486	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:49494826..49497610-chr10:49513560..49515926,2	MCF-7	breast:
2	chr10:49489462..49491590-chr10:49496144..49498930,2	MCF-7	breast:
3	chr10:49422440..49425186-chr10:49494550..49500073,5	MCF-7	breast:

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

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10745265	0.93[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs10776589	0.86[EUR][1000 genomes]
rs10776590	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10776591	0.94[ASN][1000 genomes]
rs10776592	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs10776594	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs10857554	0.94[ASN][1000 genomes]
rs10857564	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs10857565	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs11101280	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101281	0.99[ASN][1000 genomes]
rs11101282	0.94[ASN][1000 genomes]
rs11101285	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1112268	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs11597435	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs11598320	0.86[JPT][hapmap]
rs12358297	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs17697978	1.00[YRI][hapmap]
rs17698002	1.00[YRI][hapmap]
rs17698086	1.00[YRI][hapmap]
rs17780725	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs17836191	1.00[YRI][hapmap]
rs1881735	0.87[JPT][hapmap]
rs1881737	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1881740	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs1881741	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs1881742	0.89[EUR][1000 genomes]
rs1919706	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs1919707	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs1919709	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs1919710	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997365	0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2377141	0.81[ASN][1000 genomes]
rs2377142	0.93[ASN][1000 genomes]
rs2377143	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[ASN][1000 genomes]
rs2377349	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs2590386	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs2590391	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs2698758	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs2698768	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2889595	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs3730161	1.00[YRI][hapmap]
rs4529852	0.93[ASN][1000 genomes]
rs4838404	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs6537559	0.93[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs7095392	0.92[ASN][1000 genomes]
rs7898026	0.93[CHB][hapmap];0.82[JPT][hapmap];0.80[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

No data

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	chr10:49495000-49498000	Enhancers	Brain Hippocampus Middle	brain
8	chr10:49495200-49496800	Enhancers	Brain Angular Gyrus	brain
9	chr10:49495200-49497800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr10:49495200-49498200	Enhancers	Brain Substantia Nigra	brain
11	chr10:49495400-49496600	Enhancers	Colon Smooth Muscle	Colon
12	chr10:49495400-49496600	Enhancers	Lung	lung
13	chr10:49495400-49496600	Enhancers	Right Ventricle	heart
14	chr10:49495400-49497000	Enhancers	Fetal Stomach	stomach
15	chr10:49495400-49497200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr10:49495400-49497200	Enhancers	Pancreas	Pancrea
17	chr10:49495400-49497400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr10:49495400-49497800	Enhancers	Brain Cingulate Gyrus	brain
19	chr10:49495400-49498200	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr10:49495400-49498800	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr10:49495400-49500400	Enhancers	Placenta	Placenta
22	chr10:49495600-49496600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:49495600-49496600	Enhancers	Rectal Smooth Muscle	rectum
24	chr10:49495600-49497000	Enhancers	Esophagus	oesophagus
25	chr10:49495600-49497800	Enhancers	Fetal Lung	lung
26	chr10:49495600-49498200	Enhancers	Brain Anterior Caudate	brain
27	chr10:49495600-49498800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr10:49495800-49496600	Enhancers	Left Ventricle	heart
29	chr10:49495800-49496600	Enhancers	HMEC	breast
30	chr10:49495800-49497200	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr10:49495800-49497800	Enhancers	Fetal Muscle Trunk	muscle
32	chr10:49495800-49498200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr10:49495800-49500400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr10:49496000-49496600	Enhancers	HepG2	liver
35	chr10:49496000-49497000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr10:49496000-49497200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:49496000-49497200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr10:49496200-49497600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr10:49496200-49497600	Weak transcription	Fetal Brain Male	brain
40	chr10:49496200-49497800	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr10:49496200-49498000	Weak transcription	Fetal Muscle Leg	muscle
42	chr10:49496400-49496800	Enhancers	Duodenum Mucosa	Duodenum
43	chr10:49496400-49497200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr10:49496400-49497200	Weak transcription	Fetal Heart	heart
45	chr10:49496400-49497400	Weak transcription	Fetal Intestine Large	intestine
46	chr10:49496400-49497600	Weak transcription	Stomach Mucosa	stomach
47	chr10:49496400-49497800	Weak transcription	NHEK	skin
48	chr10:49496400-49498000	Weak transcription	Brain Germinal Matrix	brain
49	chr10:49496400-49498800	Weak transcription	Gastric	stomach
50	chr10:49496400-49514200	Weak transcription	Right Atrium	heart

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