Variant report

Variant	rs35829996
Chromosome Location	chr19:39349657-39349658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39340086..39344915-chr19:39346091..39351622,11	MCF-7	breast:
2	chr19:39342105..39345072-chr19:39347249..39350516,4	K562	blood:

Variant related genes	Relation type
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10403012	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10411480	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10411844	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10425464	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1078734	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11668179	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11671711	0.83[ASN][1000 genomes]
rs12974488	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12977821	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2116852	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278010	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4328569	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4802928	0.84[EUR][1000 genomes]
rs7248208	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8110679	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs862454	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs862457	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs862458	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs862460	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs862461	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs862462	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs862463	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9419	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9789283	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv911673	chr19:39335274-39365401	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	esv1798153	chr19:39338663-39399277	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35829996	ECH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39343600-39359800	Weak transcription	Small Intestine	intestine
2	chr19:39343800-39352400	Weak transcription	HUVEC	blood vessel
3	chr19:39343800-39353000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr19:39343800-39353200	Weak transcription	Fetal Kidney	kidney
5	chr19:39344000-39352800	Weak transcription	Lung	lung
6	chr19:39344000-39353000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr19:39344000-39353000	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr19:39344000-39353200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr19:39344000-39353200	Weak transcription	Right Atrium	heart
10	chr19:39344200-39353000	Weak transcription	Colon Smooth Muscle	Colon
11	chr19:39344200-39356400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr19:39345000-39353200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr19:39345400-39350000	Weak transcription	K562	blood
14	chr19:39346800-39350000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:39346800-39350800	Enhancers	Primary T cells fromperipheralblood	blood
16	chr19:39346800-39351400	Enhancers	Primary B cells from cord blood	blood
17	chr19:39347200-39350400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr19:39347800-39354400	Enhancers	Placenta	Placenta
19	chr19:39348000-39350400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr19:39348000-39351600	Weak transcription	A549	lung
21	chr19:39348400-39349800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr19:39348400-39351600	Weak transcription	Adipose Nuclei	Adipose
23	chr19:39348400-39353000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:39348400-39353000	Weak transcription	Fetal Lung	lung
25	chr19:39348400-39353000	Weak transcription	HSMMtube	muscle
26	chr19:39348400-39353400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr19:39348600-39349800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:39348600-39350000	Weak transcription	Fetal Intestine Large	intestine
29	chr19:39348600-39350000	Enhancers	GM12878-XiMat	blood
30	chr19:39348600-39350000	Enhancers	HepG2	liver
31	chr19:39348600-39350200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:39348600-39352400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:39348600-39352800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr19:39348600-39353000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:39348600-39353000	Weak transcription	Fetal Thymus	thymus
36	chr19:39348600-39353000	Weak transcription	Spleen	Spleen
37	chr19:39348600-39353800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr19:39348600-39355400	Enhancers	Primary B cells from peripheral blood	blood
39	chr19:39348600-39359600	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr19:39348800-39352800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr19:39348800-39353000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr19:39348800-39353000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr19:39348800-39353000	Weak transcription	Esophagus	oesophagus
44	chr19:39348800-39353000	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr19:39348800-39353200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr19:39348800-39355000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:39349000-39350000	Weak transcription	Fetal Intestine Small	intestine
48	chr19:39349000-39350200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr19:39349000-39350600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:39349000-39351600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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