Variant report

Variant	rs10254594
Chromosome Location	chr7:97740991-97740992
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:97737661..97739310-chr7:97740344..97742596,2	MCF-7	breast:
2	chr7:97738785..97741480-chr7:97751864..97754009,2	MCF-7	breast:
3	chr7:97733859..97737866-chr7:97738343..97741740,8	K562	blood:
4	chr7:97739559..97743131-chr7:97746340..97751154,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164715	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10215815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10235547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10238491	0.82[CEU][hapmap]
rs10248229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10254691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10259449	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10275267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10499940	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10499944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12532406	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12539490	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17169406	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17169462	0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs2272184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2291748	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735253	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs3735256	0.91[EUR][1000 genomes]
rs72494441	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72615156	0.83[AFR][1000 genomes]
rs73404144	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73404162	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73406026	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73406034	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7341519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9656054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031371	chr7:97312452-98070538	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3500384	chr7:97527787-98015382	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
3	esv3500386	chr7:97527787-98015382	Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
4	nsv1017481	chr7:97597641-98041043	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv539031	chr7:97597641-98041043	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv1019531	chr7:97653880-98034129	Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv539032	chr7:97653880-98034129	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1816676	chr7:97676259-97868033	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv831066	chr7:97726879-97890550	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:97737000-97745200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:97737000-97746200	Weak transcription	Spleen	Spleen
3	chr7:97737200-97741800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:97737200-97741800	Weak transcription	Lung	lung
5	chr7:97737200-97745600	Weak transcription	Gastric	stomach
6	chr7:97737200-97746200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:97737200-97762400	Weak transcription	Aorta	Aorta
8	chr7:97737200-97764600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr7:97737400-97741800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr7:97737400-97743400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:97737400-97744400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:97737600-97741400	Enhancers	Fetal Intestine Large	intestine
13	chr7:97737600-97741600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr7:97737600-97754400	Weak transcription	HSMMtube	muscle
15	chr7:97737600-97762400	Weak transcription	Small Intestine	intestine
16	chr7:97737800-97741000	Enhancers	Fetal Intestine Small	intestine
17	chr7:97737800-97741200	Enhancers	Fetal Brain Male	brain
18	chr7:97737800-97743600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr7:97737800-97745600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:97737800-97748600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr7:97737800-97749400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr7:97737800-97751000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr7:97737800-97759600	Weak transcription	Right Ventricle	heart
24	chr7:97737800-97760800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:97737800-97767000	Weak transcription	Fetal Stomach	stomach
26	chr7:97738000-97743000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr7:97738000-97746200	Weak transcription	NHEK	skin
28	chr7:97738000-97748400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr7:97738000-97748400	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr7:97738000-97751600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr7:97738400-97742800	Weak transcription	Primary B cells from cord blood	blood
32	chr7:97738600-97741400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr7:97738600-97741400	Weak transcription	Primary T cells from cord blood	blood
34	chr7:97738600-97742800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr7:97738600-97744400	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr7:97738800-97759200	Weak transcription	Dnd41	blood
37	chr7:97739000-97741000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr7:97739000-97741000	Enhancers	K562	blood
39	chr7:97739000-97741800	Enhancers	Brain Cingulate Gyrus	brain
40	chr7:97739000-97742000	Enhancers	Brain Anterior Caudate	brain
41	chr7:97739000-97742200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr7:97739200-97741000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:97739200-97741200	Enhancers	Brain Substantia Nigra	brain
44	chr7:97739400-97741000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr7:97739400-97741000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr7:97739400-97741000	Enhancers	Fetal Heart	heart
47	chr7:97739400-97753400	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr7:97739600-97741000	Active TSS	Duodenum Mucosa	Duodenum
49	chr7:97739600-97746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr7:97739600-97752400	Weak transcription	Fetal Lung	lung

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