Variant report

Variant	rs62121814
Chromosome Location	chr19:39159729-39159730
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39152656..39156169-chr19:39159383..39162487,4	K562	blood:
2	chr19:39157029..39159931-chr19:39175100..39177737,2	K562	blood:
3	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
4	chr19:39137645..39139443-chr19:39158789..39160706,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10403540	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10404257	0.92[ASN][1000 genomes]
rs10406778	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10415219	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10415646	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10421560	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11083475	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12460849	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12462270	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13343794	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13344413	0.90[EUR][1000 genomes]
rs16972767	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279144	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2303040	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28488032	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28624276	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3745859	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3786835	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3786839	0.82[EUR][1000 genomes]
rs3786845	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3786848	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3786851	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3810341	0.97[ASN][1000 genomes]
rs55876653	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56113315	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56365761	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62121816	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62121818	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7251903	0.84[EUR][1000 genomes]
rs7252589	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7254100	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8111746	0.84[ASN][1000 genomes]
rs883394	0.82[EUR][1000 genomes]
rs883433	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs979971	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs979972	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
4	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
5	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
6	nsv960837	chr19:39156364-39162333	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39141200-39162800	Enhancers	Psoas Muscle	Psoas
2	chr19:39147400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:39147800-39160800	Enhancers	Placenta	Placenta
4	chr19:39149600-39160200	Enhancers	Pancreas	Pancrea
5	chr19:39151400-39160000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr19:39152000-39159800	Weak transcription	Dnd41	blood
7	chr19:39152400-39160000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:39152600-39160000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:39152600-39160000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr19:39152600-39162200	Enhancers	Spleen	Spleen
11	chr19:39152600-39164000	Enhancers	Liver	Liver
12	chr19:39152800-39161200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr19:39153000-39161200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr19:39153400-39161200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:39154000-39160200	Enhancers	Primary hematopoietic stem cells	blood
16	chr19:39154000-39160400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
17	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney
18	chr19:39154000-39162800	Enhancers	Small Intestine	intestine
19	chr19:39154200-39160000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr19:39154200-39162600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr19:39154400-39160200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:39154400-39161200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr19:39154600-39162000	Enhancers	Left Ventricle	heart
24	chr19:39154600-39163000	Enhancers	Right Atrium	heart
25	chr19:39154800-39163000	Genic enhancers	Fetal Intestine Small	intestine
26	chr19:39155000-39162800	Genic enhancers	Fetal Intestine Large	intestine
27	chr19:39155200-39162800	Enhancers	Brain Angular Gyrus	brain
28	chr19:39155200-39163800	Genic enhancers	NHEK	skin
29	chr19:39155400-39160000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr19:39155400-39160000	Enhancers	Brain Anterior Caudate	brain
31	chr19:39155400-39160400	Enhancers	Stomach Mucosa	stomach
32	chr19:39155400-39161000	Genic enhancers	Fetal Muscle Leg	muscle
33	chr19:39155400-39162800	Enhancers	Brain Hippocampus Middle	brain
34	chr19:39155400-39162800	Enhancers	Brain Substantia Nigra	brain
35	chr19:39155800-39160000	Enhancers	Right Ventricle	heart
36	chr19:39155800-39162400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr19:39156000-39160000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr19:39156000-39162200	Enhancers	NHDF-Ad	bronchial
39	chr19:39156000-39162800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr19:39156200-39160800	Genic enhancers	K562	blood
41	chr19:39156400-39160000	Enhancers	Rectal Smooth Muscle	rectum
42	chr19:39156400-39162800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr19:39156600-39161400	Genic enhancers	HSMM	muscle
44	chr19:39156600-39164800	Enhancers	Fetal Heart	heart
45	chr19:39156800-39160000	Genic enhancers	Duodenum Mucosa	Duodenum
46	chr19:39157200-39160000	Enhancers	Primary T cells from cord blood	blood
47	chr19:39157200-39161200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:39157200-39161200	Genic enhancers	HepG2	liver
49	chr19:39157800-39160000	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr19:39157800-39160200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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