Variant report

Variant	rs10401224
Chromosome Location	chr19:42834708-42834709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:42833386..42835408-chr19:42838058..42839654,2	MCF-7	breast:
2	chr19:42828413..42830992-chr19:42832920..42835155,3	MCF-7	breast:
3	chr19:42829584..42831234-chr19:42832691..42834785,2	MCF-7	breast:
4	chr19:42747876..42750484-chr19:42833643..42836165,2	MCF-7	breast:
5	chr19:42828328..42831615-chr19:42831862..42835415,5	K562	blood:
6	chr19:42817930..42820453-chr19:42833140..42835671,2	MCF-7	breast:
7	chr19:42833228..42835569-chr19:42840007..42841585,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000167619	Chromatin interaction
ENSG00000105429	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10402438	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10404650	1.00[EUR][1000 genomes]
rs10406800	0.86[YRI][hapmap]
rs10406972	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407155	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10407842	1.00[EUR][1000 genomes]
rs10408258	1.00[EUR][1000 genomes]
rs10409428	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10409433	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10409939	1.00[EUR][1000 genomes]
rs10410129	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10410653	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10411498	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs10411908	1.00[EUR][1000 genomes]
rs10413484	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10414056	0.85[YRI][hapmap]
rs10415478	0.85[YRI][hapmap]
rs10415999	1.00[EUR][1000 genomes]
rs10416241	0.85[YRI][hapmap]
rs10416535	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs10418312	0.87[YRI][hapmap];1.00[EUR][1000 genomes]
rs10421409	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs10421510	0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10421857	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs10422301	1.00[EUR][1000 genomes]
rs10422867	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10423812	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10423959	1.00[EUR][1000 genomes]
rs10423978	1.00[EUR][1000 genomes]
rs10424402	1.00[EUR][1000 genomes]
rs10424939	1.00[AMR][1000 genomes]
rs10425003	1.00[EUR][1000 genomes]
rs10425320	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10425783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426267	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426284	1.00[EUR][1000 genomes]
rs11878207	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs11878297	1.00[EUR][1000 genomes]
rs11879073	1.00[EUR][1000 genomes]
rs11879538	1.00[EUR][1000 genomes]
rs11880214	1.00[EUR][1000 genomes]
rs11880356	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs11882107	1.00[EUR][1000 genomes]
rs11882801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12165130	1.00[EUR][1000 genomes]
rs13343322	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs13343388	1.00[EUR][1000 genomes]
rs13343719	1.00[EUR][1000 genomes]
rs13343761	1.00[EUR][1000 genomes]
rs13343834	1.00[EUR][1000 genomes]
rs13343966	1.00[EUR][1000 genomes]
rs13346837	1.00[EUR][1000 genomes]
rs2229614	0.93[YRI][hapmap];1.00[EUR][1000 genomes]
rs28463673	1.00[EUR][1000 genomes]
rs28469564	1.00[EUR][1000 genomes]
rs28474957	1.00[EUR][1000 genomes]
rs28483598	1.00[EUR][1000 genomes]
rs28496975	1.00[EUR][1000 genomes]
rs28572784	0.85[YRI][hapmap]
rs28657829	1.00[EUR][1000 genomes]
rs28663042	1.00[EUR][1000 genomes]
rs28675019	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28675764	1.00[EUR][1000 genomes]
rs28699037	1.00[EUR][1000 genomes]
rs28711448	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28715574	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs33919763	1.00[EUR][1000 genomes]
rs35707383	1.00[EUR][1000 genomes]
rs36089262	1.00[EUR][1000 genomes]
rs59870753	1.00[EUR][1000 genomes]
rs60950516	1.00[EUR][1000 genomes]
rs7246232	1.00[EUR][1000 genomes]
rs7248473	1.00[EUR][1000 genomes]
rs7254853	1.00[EUR][1000 genomes]
rs7255343	1.00[EUR][1000 genomes]
rs7258727	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs73552879	1.00[EUR][1000 genomes]
rs73554520	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73554531	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8099885	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs8109258	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9304602	0.89[YRI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
7	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830600-42840200	Weak transcription	Aorta	Aorta
2	chr19:42830800-42840000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:42830800-42840200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:42830800-42840400	Weak transcription	Colonic Mucosa	Colon
5	chr19:42830800-42840400	Weak transcription	A549	lung
6	chr19:42830800-42840600	Weak transcription	Primary B cells from cord blood	blood
7	chr19:42830800-42841000	Weak transcription	HSMMtube	muscle
8	chr19:42830800-42851200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr19:42830800-42856400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:42830800-42867200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr19:42830800-42867600	Weak transcription	Fetal Kidney	kidney
12	chr19:42830800-42879200	Weak transcription	Small Intestine	intestine
13	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:42831000-42839400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:42831000-42840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:42831000-42840400	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:42831000-42840400	Weak transcription	Osteobl	bone
18	chr19:42831000-42843600	Weak transcription	Right Atrium	heart
19	chr19:42831000-42856200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:42831000-42860600	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr19:42831000-42874400	Weak transcription	HSMM	muscle
22	chr19:42831200-42835000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr19:42831200-42838000	Weak transcription	Esophagus	oesophagus
24	chr19:42831200-42838600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr19:42831200-42839200	Weak transcription	Thymus	Thymus
26	chr19:42831200-42839800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr19:42831200-42840000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:42831200-42840200	Weak transcription	NHLF	lung
29	chr19:42831200-42847800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:42831200-42856600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:42831200-42856800	Weak transcription	Fetal Thymus	thymus
32	chr19:42831400-42835600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr19:42831400-42837000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:42831400-42840400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr19:42831400-42840400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:42831400-42867400	Weak transcription	Fetal Heart	heart
37	chr19:42831400-42867400	Weak transcription	NHEK	skin
38	chr19:42831600-42837000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr19:42831600-42837200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:42831600-42838600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:42831600-42840000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr19:42831600-42840400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:42831600-42840600	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr19:42831600-42840800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr19:42831600-42846200	Weak transcription	Primary T cells from cord blood	blood
46	chr19:42831600-42856400	Weak transcription	HMEC	breast
47	chr19:42831600-42856600	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr19:42831600-42861800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:42831600-42882600	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr19:42831800-42835600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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