Variant report

Variant	rs9661233
Chromosome Location	chr1:173844051-173844052
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:173792231..173795076-chr1:173841193..173844127,3	K562	blood:
2	chr1:173842881..173845710-chr1:173854372..173856048,2	K562	blood:
3	chr1:173791401..173793731-chr1:173842627..173844452,2	K562	blood:

Variant related genes	Relation type
ENSG00000117593	Chromatin interaction
ENSG00000120334	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10798295	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10798301	0.91[CHB][hapmap]
rs10798302	0.87[CHB][hapmap]
rs12066153	0.87[CHB][hapmap]
rs12071594	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12071663	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12078824	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1322770	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1322775	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1322777	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1322780	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1799876	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1884994	0.83[CHB][hapmap]
rs1951627	0.87[CHB][hapmap];1.00[YRI][hapmap]
rs2065171	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4652229	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4971204	0.88[YRI][hapmap]
rs5877	0.96[CEU][hapmap];0.85[CHB][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6663875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665484	0.87[CHB][hapmap]
rs6677660	0.87[CHB][hapmap]
rs6686083	0.87[CHB][hapmap]
rs6689285	0.87[CHB][hapmap]
rs6696163	0.87[CHB][hapmap]
rs714624	0.87[CHB][hapmap]
rs7349095	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7413166	0.86[CHB][hapmap]
rs7544605	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7552939	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9286895	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs941989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9425430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425435	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425755	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9425765	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9425766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9661233		cis	Lymphoblastoid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173838200-173846600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:173838200-173854200	Weak transcription	Gastric	stomach
3	chr1:173838200-173866000	Weak transcription	Small Intestine	intestine
4	chr1:173838400-173844600	Weak transcription	Ovary	ovary
5	chr1:173838400-173844800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:173838400-173854200	Weak transcription	Esophagus	oesophagus
7	chr1:173838400-173854800	Weak transcription	Aorta	Aorta
8	chr1:173838400-173854800	Weak transcription	Right Ventricle	heart
9	chr1:173838400-173860200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:173838600-173854800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:173838800-173844400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:173838800-173855800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr1:173839000-173848400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:173839000-173850000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr1:173839000-173854800	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:173839000-173862800	Weak transcription	HMEC	breast
17	chr1:173839200-173850000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:173839200-173855000	Weak transcription	A549	lung
19	chr1:173839400-173847800	Strong transcription	Fetal Muscle Trunk	muscle
20	chr1:173839400-173847800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr1:173839400-173849200	Strong transcription	Fetal Stomach	stomach
22	chr1:173839400-173850000	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:173839600-173854600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:173839800-173845400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr1:173840000-173845400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:173840200-173844200	Weak transcription	Left Ventricle	heart
27	chr1:173840200-173845800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr1:173840200-173849600	Strong transcription	Placenta	Placenta
29	chr1:173840200-173854200	Weak transcription	Colonic Mucosa	Colon
30	chr1:173840200-173854800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr1:173840200-173856800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:173840400-173845800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr1:173840400-173846400	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr1:173840400-173846400	Weak transcription	Brain Germinal Matrix	brain
35	chr1:173840400-173846400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:173840400-173855000	Weak transcription	Psoas Muscle	Psoas
37	chr1:173840600-173844600	Weak transcription	NHEK	skin
38	chr1:173840600-173844800	Weak transcription	Fetal Intestine Small	intestine
39	chr1:173840600-173849400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr1:173840600-173854200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr1:173840800-173844600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr1:173840800-173844600	Weak transcription	Spleen	Spleen
43	chr1:173840800-173844800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:173840800-173844800	Weak transcription	Brain Hippocampus Middle	brain
45	chr1:173840800-173844800	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr1:173840800-173844800	Weak transcription	Lung	lung
47	chr1:173840800-173844800	Weak transcription	Pancreas	Pancrea
48	chr1:173840800-173844800	Weak transcription	Thymus	Thymus
49	chr1:173840800-173844800	Weak transcription	HSMMtube	muscle
50	chr1:173840800-173846600	Weak transcription	Fetal Thymus	thymus

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