Variant report

Variant	rs1985636
Chromosome Location	chr19:39159278-39159279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39157029..39159931-chr19:39175100..39177737,2	K562	blood:
2	chr19:39156941..39159370-chr19:39200344..39202279,2	MCF-7	breast:
3	chr19:39149024..39154711-chr19:39158901..39163144,7	MCF-7	breast:
4	chr19:39137645..39139443-chr19:39158789..39160706,2	MCF-7	breast:
5	chr19:39157020..39159393-chr19:39170595..39173839,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1031849	0.82[ASN][1000 genomes]
rs10424568	0.96[ASN][1000 genomes]
rs11665964	0.83[ASN][1000 genomes]
rs12462503	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12984247	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1564203	0.83[ASN][1000 genomes]
rs2080988	0.84[ASN][1000 genomes]
rs2112649	0.84[ASN][1000 genomes]
rs2112651	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3786841	0.83[ASN][1000 genomes]
rs3786843	0.82[ASN][1000 genomes]
rs4347742	0.84[ASN][1000 genomes]
rs4802743	0.84[ASN][1000 genomes]
rs6508813	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6508814	0.85[ASN][1000 genomes]
rs7252630	0.84[ASN][1000 genomes]
rs749701	0.82[ASN][1000 genomes]
rs752067	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs755690	0.85[ASN][1000 genomes]
rs8099948	0.83[ASN][1000 genomes]
rs888996	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs888997	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9304576	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1985636	CAPN12	cis	Adipose Subcutaneous	GTEx
rs1985636	CAPN12	cis	Esophagus Muscularis	GTEx
rs1985636	CTD-2540F13.2	cis	Nerve Tibial	GTEx

Chromatin state (count:126 , 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	chr19:39152800-39159400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr19:39152800-39161200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:39153000-39161200	Enhancers	Placenta Amnion	Placenta Amnion
15	chr19:39153400-39159400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:39153400-39161200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:39154000-39160200	Enhancers	Primary hematopoietic stem cells	blood
18	chr19:39154000-39160400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
19	chr19:39154000-39162600	Enhancers	Fetal Kidney	kidney
20	chr19:39154000-39162800	Enhancers	Small Intestine	intestine
21	chr19:39154200-39160000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr19:39154200-39162600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:39154400-39160200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:39154400-39161200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr19:39154600-39162000	Enhancers	Left Ventricle	heart
26	chr19:39154600-39163000	Enhancers	Right Atrium	heart
27	chr19:39154800-39163000	Genic enhancers	Fetal Intestine Small	intestine
28	chr19:39155000-39162800	Genic enhancers	Fetal Intestine Large	intestine
29	chr19:39155200-39162800	Enhancers	Brain Angular Gyrus	brain
30	chr19:39155200-39163800	Genic enhancers	NHEK	skin
31	chr19:39155400-39160000	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr19:39155400-39160000	Enhancers	Brain Anterior Caudate	brain
33	chr19:39155400-39160400	Enhancers	Stomach Mucosa	stomach
34	chr19:39155400-39161000	Genic enhancers	Fetal Muscle Leg	muscle
35	chr19:39155400-39162800	Enhancers	Brain Hippocampus Middle	brain
36	chr19:39155400-39162800	Enhancers	Brain Substantia Nigra	brain
37	chr19:39155800-39160000	Enhancers	Right Ventricle	heart
38	chr19:39155800-39162400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
39	chr19:39156000-39160000	Enhancers	Primary T cells fromperipheralblood	blood
40	chr19:39156000-39162200	Enhancers	NHDF-Ad	bronchial
41	chr19:39156000-39162800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:39156200-39160800	Genic enhancers	K562	blood
43	chr19:39156400-39160000	Enhancers	Rectal Smooth Muscle	rectum
44	chr19:39156400-39162800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:39156600-39161400	Genic enhancers	HSMM	muscle
46	chr19:39156600-39164800	Enhancers	Fetal Heart	heart
47	chr19:39156800-39160000	Genic enhancers	Duodenum Mucosa	Duodenum
48	chr19:39157200-39160000	Enhancers	Primary T cells from cord blood	blood
49	chr19:39157200-39161200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39157200-39161200	Genic enhancers	HepG2	liver

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