Variant report

Variant	rs6540935
Chromosome Location	chr1:10571841-10571842
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10570510..10573214-chr1:10855273..10856908,2	MCF-7	breast:
2	chr1:10566900..10569422-chr1:10571271..10572995,2	K562	blood:
3	chr1:10570193..10573088-chr1:10575798..10579645,3	MCF-7	breast:
4	chr1:10570481..10573299-chr1:10599222..10600978,2	K562	blood:
5	chr1:10571375..10572978-chr1:10573706..10575534,2	K562	blood:
6	chr1:10552985..10554515-chr1:10570159..10573130,2	K562	blood:

Variant related genes	Relation type
ENSG00000130940	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10436982	0.86[EUR][1000 genomes]
rs12057729	1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs12063215	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12090079	0.91[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12091086	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13375411	0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17034849	1.00[MEX][hapmap]
rs17035154	0.91[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2274986	1.00[CEU][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2297881	1.00[MEX][hapmap]
rs28522839	0.86[EUR][1000 genomes]
rs28663566	0.85[EUR][1000 genomes]
rs57986045	1.00[EUR][1000 genomes]
rs61776020	0.86[EUR][1000 genomes]
rs61776039	0.86[EUR][1000 genomes]
rs61776041	0.86[EUR][1000 genomes]
rs61776042	0.86[EUR][1000 genomes]
rs61776043	0.86[EUR][1000 genomes]
rs61776045	0.93[EUR][1000 genomes]
rs61776260	1.00[EUR][1000 genomes]
rs61776261	1.00[EUR][1000 genomes]
rs61777175	0.86[EUR][1000 genomes]
rs61777176	0.86[EUR][1000 genomes]
rs61777177	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs61777178	0.86[EUR][1000 genomes]
rs61777205	1.00[EUR][1000 genomes]
rs61777209	1.00[EUR][1000 genomes]
rs6540934	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664032	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6668910	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6679456	0.93[EUR][1000 genomes]
rs6680568	1.00[CEU][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs7512333	0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7524983	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7534960	1.00[EUR][1000 genomes]
rs7551790	1.00[EUR][1000 genomes]
rs9661820	0.86[EUR][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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv2521	chr1:10553530-10598171	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv8435	chr1:10568184-10572374	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10566400-10577800	Enhancers	Fetal Thymus	thymus
2	chr1:10566800-10579800	Enhancers	Liver	Liver
3	chr1:10567400-10572600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr1:10567600-10572200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:10568400-10572400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:10568800-10573800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:10568800-10576600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:10569000-10573600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr1:10569000-10578800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:10569600-10572800	Enhancers	HMEC	breast
11	chr1:10569600-10577800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:10569800-10573600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr1:10569800-10575000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:10570000-10572000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr1:10570000-10572000	Enhancers	Esophagus	oesophagus
16	chr1:10570000-10572000	Enhancers	Psoas Muscle	Psoas
17	chr1:10570000-10572000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr1:10570000-10572000	Enhancers	Spleen	Spleen
19	chr1:10570000-10572600	Enhancers	Duodenum Mucosa	Duodenum
20	chr1:10570000-10572600	Flanking Active TSS	Dnd41	blood
21	chr1:10570000-10573800	Enhancers	Fetal Intestine Large	intestine
22	chr1:10570200-10572000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:10570200-10572200	Enhancers	Thymus	Thymus
24	chr1:10570200-10572600	Genic enhancers	Fetal Intestine Small	intestine
25	chr1:10570200-10574400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr1:10570400-10572000	Enhancers	Primary B cells from peripheral blood	blood
27	chr1:10570400-10572000	Flanking Active TSS	NHLF	lung
28	chr1:10570400-10572200	Enhancers	Brain Anterior Caudate	brain
29	chr1:10570400-10572200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr1:10570600-10572000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:10570600-10572000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:10570600-10572000	Flanking Active TSS	GM12878-XiMat	blood
33	chr1:10570600-10572400	Enhancers	Lung	lung
34	chr1:10570800-10574400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:10570800-10574400	Weak transcription	Fetal Heart	heart
36	chr1:10570800-10579800	Weak transcription	Aorta	Aorta
37	chr1:10570800-10595600	Weak transcription	Primary B cells from cord blood	blood
38	chr1:10571000-10572000	Enhancers	Colon Smooth Muscle	Colon
39	chr1:10571000-10572000	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr1:10571000-10572800	Enhancers	Skeletal Muscle Female	skeletal muscle
41	chr1:10571000-10573400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:10571000-10573400	Weak transcription	Fetal Stomach	stomach
43	chr1:10571000-10573600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:10571000-10574400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:10571000-10574400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr1:10571000-10574800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr1:10571000-10574800	Weak transcription	Brain Germinal Matrix	brain
48	chr1:10571000-10576000	Weak transcription	Brain Hippocampus Middle	brain
49	chr1:10571000-10576600	Weak transcription	Placenta	Placenta
50	chr1:10571000-10577000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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