Variant report

Variant	rs6704010
Chromosome Location	chr1:180246451-180246452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:180246139-180246481	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:180245403..180247439-chr1:180257140..180259358,2	MCF-7	breast:
2	chr1:180245366..180247514-chr1:180249849..180251936,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230124	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10494527	0.81[CEU][hapmap]
rs10753211	0.81[CEU][hapmap]
rs10798746	0.81[CEU][hapmap]
rs10798759	0.81[CEU][hapmap]
rs10798762	0.81[CEU][hapmap]
rs10798769	0.81[CEU][hapmap]
rs10913980	0.81[CEU][hapmap]
rs10913981	0.81[CEU][hapmap]
rs10913985	0.81[CEU][hapmap]
rs10913987	0.81[CEU][hapmap]
rs10914005	0.81[CEU][hapmap]
rs12034217	0.81[CEU][hapmap]
rs12141348	0.80[CEU][hapmap]
rs12730889	0.81[CEU][hapmap]
rs2296378	0.81[CEU][hapmap]
rs4076403	0.81[CEU][hapmap]
rs4421553	0.81[CEU][hapmap]
rs4578179	0.81[CEU][hapmap]
rs4652493	0.81[CEU][hapmap]
rs6665719	0.81[CEU][hapmap]
rs6670544	0.81[CEU][hapmap]
rs6680361	0.83[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6697924	0.81[CEU][hapmap]
rs7528650	0.81[CEU][hapmap]
rs7532806	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1005073	chr1:180152550-180250783	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv535219	chr1:180152550-180250783	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6704010	ACBD6	cis	parietal	SCAN
rs6704010	CACYBP	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180231000-180257200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:180236200-180252200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr1:180236400-180249800	Weak transcription	Hela-S3	cervix
4	chr1:180236800-180257600	Weak transcription	Fetal Brain Male	brain
5	chr1:180238600-180255600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:180239200-180257200	Weak transcription	Osteobl	bone
7	chr1:180239400-180249600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr1:180240200-180259000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:180240400-180246600	Weak transcription	Fetal Thymus	thymus
10	chr1:180240600-180255600	Weak transcription	Liver	Liver
11	chr1:180240800-180247400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:180240800-180249400	Weak transcription	Left Ventricle	heart
13	chr1:180240800-180258200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr1:180240800-180259400	Weak transcription	HepG2	liver
15	chr1:180240800-180264000	Weak transcription	Small Intestine	intestine
16	chr1:180240800-180270800	Weak transcription	NHLF	lung
17	chr1:180241000-180254800	Weak transcription	HMEC	breast
18	chr1:180241000-180259600	Weak transcription	NH-A	brain
19	chr1:180241200-180257000	Weak transcription	K562	blood
20	chr1:180241400-180247400	Weak transcription	HUVEC	blood vessel
21	chr1:180241400-180247600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:180241400-180247600	Weak transcription	Brain Anterior Caudate	brain
23	chr1:180241400-180250800	Strong transcription	Primary T cells from cord blood	blood
24	chr1:180241600-180247600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr1:180241600-180251000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:180242000-180247400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:180242000-180268400	Weak transcription	NHDF-Ad	bronchial
28	chr1:180242600-180257200	Weak transcription	Brain Substantia Nigra	brain
29	chr1:180243000-180247800	Strong transcription	Dnd41	blood
30	chr1:180243200-180247800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:180243600-180246800	Strong transcription	Primary B cells from peripheral blood	blood
32	chr1:180243600-180257200	Weak transcription	GM12878-XiMat	blood
33	chr1:180243800-180255400	Weak transcription	Fetal Brain Female	brain
34	chr1:180243800-180268200	Weak transcription	Pancreas	Pancrea
35	chr1:180244000-180251600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:180244000-180257200	Weak transcription	Brain Hippocampus Middle	brain
37	chr1:180244000-180257400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:180244200-180257200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:180244200-180257800	Weak transcription	Brain Germinal Matrix	brain
40	chr1:180244200-180258200	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:180244200-180258400	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:180244200-180263000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr1:180244200-180270400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr1:180244200-180278200	Weak transcription	HSMMtube	muscle
45	chr1:180244400-180246800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:180244600-180247200	Weak transcription	Thymus	Thymus
47	chr1:180244600-180249600	Weak transcription	A549	lung
48	chr1:180244600-180252400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:180244600-180257600	Weak transcription	Fetal Kidney	kidney
50	chr1:180244800-180247200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links