Variant report

Variant	rs2689677
Chromosome Location	chr1:77687977-77687978
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	chr1:77687932-77687996	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:77687960-77688006	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77677424..77679474-chr1:77687776..77689660,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AK5-1	chr1:77686286-77690011	NONHSAT004022

Variant related genes	Relation type
PIGK	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1098131	0.81[AFR][1000 genomes]
rs1419248	1.00[AFR][1000 genomes]
rs1779191	0.90[AFR][1000 genomes]
rs2247900	0.81[AFR][1000 genomes]
rs2653467	0.81[AFR][1000 genomes]
rs2689681	0.90[AFR][1000 genomes]
rs7414972	0.81[AFR][1000 genomes]
rs839796	1.00[YRI][hapmap]
rs839801	0.90[AFR][1000 genomes]
rs839803	0.90[AFR][1000 genomes]
rs839804	0.90[AFR][1000 genomes]
rs839815	1.00[AFR][1000 genomes]
rs839816	1.00[AFR][1000 genomes]
rs839825	0.90[AFR][1000 genomes]
rs839828	1.00[YRI][hapmap]
rs839829	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs839832	0.90[AFR][1000 genomes]
rs839836	0.90[AFR][1000 genomes]
rs865742	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006887	chr1:77566348-77698128	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv520629	chr1:77584846-77695854	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv525188	chr1:77655651-77695854	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77685400-77688000	Weak transcription	Gastric	stomach
2	chr1:77685400-77689600	Weak transcription	Esophagus	oesophagus
3	chr1:77685600-77693400	Weak transcription	Pancreas	Pancrea
4	chr1:77685800-77688400	Weak transcription	Right Atrium	heart
5	chr1:77685800-77688600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr1:77685800-77688600	Weak transcription	Fetal Thymus	thymus
7	chr1:77685800-77688600	Weak transcription	Psoas Muscle	Psoas
8	chr1:77685800-77688800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:77685800-77689000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:77685800-77689600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:77685800-77689600	Weak transcription	Ovary	ovary
12	chr1:77685800-77690000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr1:77685800-77692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr1:77685800-77695600	Weak transcription	Left Ventricle	heart
15	chr1:77686000-77688000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr1:77686000-77688000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:77686000-77688000	Weak transcription	Fetal Intestine Large	intestine
18	chr1:77686000-77688000	Weak transcription	Fetal Intestine Small	intestine
19	chr1:77686000-77688600	Weak transcription	Fetal Brain Female	brain
20	chr1:77686000-77688600	Weak transcription	Right Ventricle	heart
21	chr1:77686000-77689000	Weak transcription	HSMM	muscle
22	chr1:77686000-77689600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:77686000-77689600	Weak transcription	Thymus	Thymus
24	chr1:77686000-77690600	Weak transcription	Primary B cells from cord blood	blood
25	chr1:77686000-77690800	Weak transcription	Fetal Brain Male	brain
26	chr1:77686000-77691600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr1:77686000-77692200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:77686000-77692400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr1:77686000-77694600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:77686000-77694600	Weak transcription	Fetal Kidney	kidney
31	chr1:77686000-77699200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:77686200-77688000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:77686200-77688800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr1:77686200-77689000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:77686200-77689600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr1:77686200-77690200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:77686400-77688400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
38	chr1:77686600-77688000	Weak transcription	Liver	Liver
39	chr1:77686600-77688400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr1:77686600-77688400	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:77686600-77688600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:77686600-77689800	Weak transcription	Osteobl	bone
43	chr1:77686600-77691200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr1:77686600-77693000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:77686600-77693200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:77686600-77694600	Weak transcription	A549	lung
47	chr1:77686600-77694800	Weak transcription	Brain Hippocampus Middle	brain
48	chr1:77686600-77698200	Weak transcription	Brain Angular Gyrus	brain
49	chr1:77686800-77688400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:77686800-77689400	Weak transcription	Primary T helper cells PMA-I stimulated	--

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