Variant report

Variant	rs3130662
Chromosome Location	chr6:30713808-30713809
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30581322..30587794-chr6:30705649..30714068,32	K562	blood:
2	chr6:30703666..30722133-chr6:30776009..30801352,184	MCF-7	breast:
3	chr6:30707481..30713943-chr6:30872979..30880006,10	MCF-7	breast:
4	chr6:30705171..30717521-chr6:30843972..30856100,74	MCF-7	breast:
5	chr6:30580645..30587403-chr6:30708153..30714600,16	MCF-7	breast:
6	chr6:30704403..30722478-chr6:30842859..30858629,100	MCF-7	breast:
7	chr6:30703055..30723531-chr6:30783853..30800217,151	MCF-7	breast:
8	chr6:30710424..30713995-chr6:30746295..30752430,9	K562	blood:
9	chr6:30707880..30713865-chr6:30880456..30883497,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000213780	Chromatin interaction
ENSG00000264731	Chromatin interaction
ENSG00000214894	Chromatin interaction
ENSG00000228022	Chromatin interaction
ENSG00000204580	Chromatin interaction
ENSG00000222894	Chromatin interaction
ENSG00000137411	Chromatin interaction
ENSG00000204568	Chromatin interaction
ENSG00000237775	Chromatin interaction
ENSG00000204569	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1049943	1.00[ASN][1000 genomes]
rs1061397	1.00[ASN][1000 genomes]
rs1061424	0.94[ASN][1000 genomes]
rs1064627	0.86[EUR][1000 genomes]
rs10947088	1.00[ASN][1000 genomes]
rs10947089	1.00[ASN][1000 genomes]
rs1136719	1.00[ASN][1000 genomes]
rs12111310	0.97[ASN][1000 genomes]
rs1264352	0.83[ASN][1000 genomes]
rs15297	1.00[ASN][1000 genomes]
rs17189329	0.85[ASN][1000 genomes]
rs17195712	1.00[ASN][1000 genomes]
rs17719	1.00[ASN][1000 genomes]
rs28600807	1.00[ASN][1000 genomes]
rs3094128	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3909184	1.00[ASN][1000 genomes]
rs41270529	1.00[ASN][1000 genomes]
rs58638768	1.00[ASN][1000 genomes]
rs9968884	1.00[ASN][1000 genomes]
rs9968888	1.00[ASN][1000 genomes]
rs9968913	1.00[ASN][1000 genomes]
rs9968960	1.00[ASN][1000 genomes]
rs9969042	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription 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	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	esv3430377	chr6:30443802-30814426	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers 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 miRNA target site	967 gene(s)	inside rSNPs	diseases
5	nsv830626	chr6:30558064-30732905	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	406 gene(s)	inside rSNPs	diseases
6	esv2758041	chr6:30644693-30816319	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
7	esv2759413	chr6:30644693-30816319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	223 gene(s)	inside rSNPs	diseases
8	nsv884100	chr6:30693816-30751326	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
9	nsv884101	chr6:30695920-30733121	Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	163 gene(s)	inside rSNPs	diseases
10	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
11	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
12	nsv884102	chr6:30706013-30720567	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
13	nsv870418	chr6:30713196-30755668	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3130662	HLA-C	Cis_1M	lymphoblastoid	RTeQTL
rs3130662	TUBB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30712200-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:30712400-30715200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr6:30712400-30715200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:30712400-30715400	Weak transcription	Small Intestine	intestine
5	chr6:30712400-30715600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr6:30712400-30715800	Weak transcription	Lung	lung
7	chr6:30712600-30714600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:30712600-30714800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:30712600-30715200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr6:30712600-30715200	Weak transcription	Gastric	stomach
11	chr6:30712600-30715200	Enhancers	HepG2	liver
12	chr6:30712600-30715200	Weak transcription	HSMM	muscle
13	chr6:30712600-30715200	Weak transcription	NHDF-Ad	bronchial
14	chr6:30712600-30715400	Weak transcription	Primary T cells from cord blood	blood
15	chr6:30712600-30715400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr6:30712600-30715600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:30712600-30715800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:30712600-30715800	Weak transcription	Left Ventricle	heart
19	chr6:30712600-30715800	Weak transcription	Thymus	Thymus
20	chr6:30712600-30715800	Enhancers	NHEK	skin
21	chr6:30712600-30716200	Weak transcription	HSMMtube	muscle
22	chr6:30712600-30716400	Weak transcription	Ovary	ovary
23	chr6:30712600-30716400	Enhancers	Stomach Mucosa	stomach
24	chr6:30712600-30716400	Enhancers	HUVEC	blood vessel
25	chr6:30712600-30719400	Weak transcription	Brain Anterior Caudate	brain
26	chr6:30712600-30719400	Weak transcription	Psoas Muscle	Psoas
27	chr6:30712600-30719600	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:30712600-30719600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr6:30712600-30724000	Enhancers	HMEC	breast
30	chr6:30712800-30714000	Enhancers	K562	blood
31	chr6:30712800-30715000	Weak transcription	Osteobl	bone
32	chr6:30712800-30715200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:30712800-30715200	Weak transcription	Fetal Intestine Large	intestine
34	chr6:30712800-30715400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:30712800-30715400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr6:30712800-30715600	Weak transcription	Fetal Kidney	kidney
37	chr6:30712800-30716400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr6:30712800-30716400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr6:30712800-30716400	Weak transcription	Fetal Lung	lung
40	chr6:30712800-30716600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:30712800-30716600	Weak transcription	Liver	Liver
42	chr6:30712800-30716600	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr6:30712800-30717600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr6:30712800-30718400	Weak transcription	Rectal Smooth Muscle	rectum
45	chr6:30712800-30719400	Weak transcription	Right Ventricle	heart
46	chr6:30712800-30720000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:30713000-30714000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:30713000-30715200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr6:30713000-30715400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:30713000-30715800	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links