Variant report

Variant	rs419788
Chromosome Location	chr6:31928799-31928800
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:31631207..31634109-chr6:31926807..31929140,3	K562	blood:
2	chr6:31864040..31872511-chr6:31917614..31930102,27	MCF-7	breast:
3	chr6:31867895..31873109-chr6:31925613..31930389,7	K562	blood:
4	chr6:31800911..31802775-chr6:31927377..31929247,2	MCF-7	breast:
5	chr6:31886651..31888947-chr6:31926731..31929141,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204371	Chromatin interaction
ENSG00000204438	Chromatin interaction
ENSG00000204435	Chromatin interaction
ENSG00000204387	Chromatin interaction
ENSG00000204366	Chromatin interaction
ENSG00000263020	Chromatin interaction
ENSG00000166278	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs386480	0.98[EUR][1000 genomes]
rs389883	0.98[EUR][1000 genomes]
rs410851	0.98[EUR][1000 genomes]
rs437179	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs440454	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537160	0.81[EUR][1000 genomes]
rs630379	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv601610	chr6:31280101-31960770	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	370 gene(s)	inside rSNPs	diseases
2	nsv601628	chr6:31280327-31990098	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
3	nsv601629	chr6:31280327-31996185	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
4	nsv601630	chr6:31280327-32011317	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
5	nsv601631	chr6:31280327-32017540	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	378 gene(s)	inside rSNPs	diseases
6	nsv1023939	chr6:31325961-32026747	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
7	nsv538188	chr6:31325961-32026747	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	372 gene(s)	inside rSNPs	diseases
8	nsv1033154	chr6:31550614-32009410	Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	326 gene(s)	inside rSNPs	diseases
9	nsv1017945	chr6:31609641-32481240	Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
10	nsv601950	chr6:31785438-32492308	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
11	nsv601951	chr6:31785438-32496748	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
12	nsv601955	chr6:31785453-32484368	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
13	nsv601956	chr6:31785453-32492308	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	197 gene(s)	inside rSNPs	diseases
14	nsv601961	chr6:31868322-32484368	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
15	nsv427751	chr6:31871512-32092843	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
16	nsv428141	chr6:31871512-32092843	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
17	esv2758043	chr6:31871512-32209113	Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
18	esv2759415	chr6:31871512-32209113	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
19	nsv830628	chr6:31887554-31947600	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
20	nsv933250	chr6:31905060-32008005	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
21	nsv934279	chr6:31905060-32013902	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
22	nsv884512	chr6:31908470-31933161	Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
23	nsv884513	chr6:31922575-32066025	Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
24	nsv884514	chr6:31923052-31958960	Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
25	nsv932869	chr6:31924496-32013902	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
26	nsv933913	chr6:31924682-32009282	Active TSS Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
27	nsv284	chr6:31925739-31996721	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong 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 target site	61 gene(s)	inside rSNPs	diseases
28	nsv5247	chr6:31925739-32023216	Transcr. at gene 5' and 3' Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs419788	HLA-DRB5	cis	cerebellum	SCAN
rs419788	HMGA1	cis	cerebellum	SCAN
rs419788	SKIV2L	cis	lymphoblastoid	seeQTL
rs419788	HLA-C	cis	lymphoblastoid	GTEx
rs419788	HLA-DRB5	cis	lymphoblastoid	seeQTL
rs419788	HLA-DRB1	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31927400-31928800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:31927400-31928800	Weak transcription	Aorta	Aorta
3	chr6:31927400-31929600	Weak transcription	Psoas Muscle	Psoas
4	chr6:31927400-31938800	Weak transcription	Right Atrium	heart
5	chr6:31927600-31928800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:31927600-31929000	Weak transcription	Left Ventricle	heart
7	chr6:31927600-31929400	Genic enhancers	Primary T cells fromperipheralblood	blood
8	chr6:31927600-31937000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:31927600-31939400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr6:31927800-31928800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr6:31927800-31928800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:31927800-31929200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:31927800-31929400	Weak transcription	Small Intestine	intestine
14	chr6:31927800-31929400	Weak transcription	HSMMtube	muscle
15	chr6:31927800-31929400	Weak transcription	HUVEC	blood vessel
16	chr6:31927800-31934800	Weak transcription	Fetal Heart	heart
17	chr6:31927800-31935400	Weak transcription	Stomach Mucosa	stomach
18	chr6:31927800-31937000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr6:31927800-31938400	Strong transcription	Lung	lung
20	chr6:31927800-31938600	Strong transcription	NHEK	skin
21	chr6:31928000-31928800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:31928000-31928800	Weak transcription	Brain Germinal Matrix	brain
23	chr6:31928000-31929000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr6:31928000-31929000	Weak transcription	Pancreas	Pancrea
25	chr6:31928000-31932400	Strong transcription	NHDF-Ad	bronchial
26	chr6:31928000-31936200	Strong transcription	Stomach Smooth Muscle	stomach
27	chr6:31928000-31936800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:31928000-31937200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:31928000-31937200	Strong transcription	Fetal Brain Female	brain
30	chr6:31928000-31937400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:31928000-31937400	Strong transcription	Brain Inferior Temporal Lobe	brain
32	chr6:31928000-31937600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:31928000-31937800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:31928000-31937800	Strong transcription	Brain Cingulate Gyrus	brain
35	chr6:31928000-31937800	Strong transcription	Brain Hippocampus Middle	brain
36	chr6:31928000-31937800	Strong transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:31928000-31938000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:31928000-31938000	Strong transcription	Fetal Stomach	stomach
39	chr6:31928000-31938200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr6:31928000-31938200	Strong transcription	Fetal Intestine Small	intestine
41	chr6:31928000-31938200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr6:31928000-31938200	Strong transcription	Placenta	Placenta
43	chr6:31928000-31938200	Strong transcription	Ovary	ovary
44	chr6:31928000-31938200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr6:31928000-31938400	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:31928000-31938400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:31928000-31938400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr6:31928000-31938400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr6:31928000-31938400	Strong transcription	Fetal Muscle Leg	muscle
50	chr6:31928000-31938600	Strong transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links