Variant report

Variant	rs6683840
Chromosome Location	chr1:92249817-92249818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:92249408..92251334-chr1:92252607..92255578,2	K562	blood:
2	chr1:92242856..92244541-chr1:92248702..92251001,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10874940	0.89[CHB][hapmap]
rs10874941	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874976	0.89[CHB][hapmap]
rs11165489	0.89[CHB][hapmap]
rs11165496	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11165532	0.94[CHB][hapmap]
rs11466573	0.89[ASN][1000 genomes]
rs1192530	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12090296	0.89[CHB][hapmap]
rs12756024	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1411276	0.89[CHB][hapmap]
rs1473486	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1473488	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1473767	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2171584	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297142	0.93[CHB][hapmap]
rs2391068	0.89[CHB][hapmap]
rs2391069	0.88[CHB][hapmap]
rs4658113	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4658268	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs5019497	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs6604054	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6604055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6604056	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs6669044	0.88[CHB][hapmap]
rs6678564	0.93[CHB][hapmap]
rs6691098	0.89[CHB][hapmap]
rs7521065	0.81[CHB][hapmap]
rs7530883	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7534318	0.88[CHB][hapmap]
rs7536947	0.89[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1005917	chr1:92189945-92378683	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv949449	chr1:92211020-92585831	Strong transcription Enhancers Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv524845	chr1:92215725-92598705	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv462517	chr1:92215725-92598705	Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv546810	chr1:92215725-92598705	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1006318	chr1:92216408-92608324	Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv432498	chr1:92218245-92618323	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv1004570	chr1:92220544-92622129	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
15	nsv1007661	chr1:92220544-92655952	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv1014837	chr1:92233905-92618839	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
17	nsv535031	chr1:92233905-92618839	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv1012134	chr1:92235485-92598800	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
19	nsv546818	chr1:92236048-92579206	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6683840	LRRC8D	cis	cerebellum	SCAN
rs6683840	GFI1	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92220600-92255800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:92227000-92257200	Weak transcription	Fetal Intestine Small	intestine
3	chr1:92233200-92257000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:92241400-92255800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr1:92241800-92255800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:92243600-92250200	Weak transcription	Psoas Muscle	Psoas
7	chr1:92244000-92253600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr1:92244600-92255200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:92244600-92257200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:92244800-92251000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr1:92245200-92261200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:92245400-92254200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:92245600-92254000	Weak transcription	Brain Anterior Caudate	brain
14	chr1:92245600-92258400	Weak transcription	Brain Angular Gyrus	brain
15	chr1:92245800-92255200	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr1:92246000-92255400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:92246200-92250600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr1:92246200-92250600	Enhancers	Colon Smooth Muscle	Colon
19	chr1:92246200-92251000	Enhancers	HUVEC	blood vessel
20	chr1:92246400-92250000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr1:92246600-92250000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:92246600-92251200	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr1:92246800-92257800	Genic enhancers	NHDF-Ad	bronchial
24	chr1:92247000-92250400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:92247000-92250400	Enhancers	Osteobl	bone
26	chr1:92247400-92250000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:92247400-92250600	Weak transcription	K562	blood
28	chr1:92247400-92255800	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:92247600-92251000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr1:92247800-92251600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:92248200-92256000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr1:92248200-92268800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:92248600-92262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:92248600-92268800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:92248800-92250200	Enhancers	Fetal Kidney	kidney
36	chr1:92248800-92250400	Enhancers	Brain Hippocampus Middle	brain
37	chr1:92248800-92250600	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:92248800-92251000	Enhancers	Adipose Nuclei	Adipose
39	chr1:92249000-92250000	Weak transcription	Fetal Heart	heart
40	chr1:92249000-92250400	Enhancers	NHLF	lung
41	chr1:92249000-92250600	Enhancers	Fetal Muscle Leg	muscle
42	chr1:92249000-92250800	Genic enhancers	HepG2	liver
43	chr1:92249000-92254000	Weak transcription	Liver	Liver
44	chr1:92249000-92256800	Weak transcription	Small Intestine	intestine
45	chr1:92249000-92257200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:92249000-92257200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:92249000-92257200	Weak transcription	Esophagus	oesophagus
48	chr1:92249200-92250400	Enhancers	Fetal Lung	lung
49	chr1:92249200-92250400	Enhancers	Fetal Stomach	stomach
50	chr1:92249200-92250800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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