Variant report

Variant	rs6431659
Chromosome Location	chr2:234167020-234167021
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234166526..234169177-chr2:234198735..234200810,2	MCF-7	breast:
2	chr2:234166864..234169330-chr2:234170914..234172883,2	K562	blood:
3	chr2:234161323..234164097-chr2:234164693..234167813,4	K562	blood:
4	chr2:234161693..234166047-chr2:234167019..234170688,4	MCF-7	breast:
5	chr2:234158513..234163302-chr2:234165991..234171009,7	K562	blood:

Variant related genes	Relation type
ENSG00000085978	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1045095	0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap]
rs10929033	0.86[ASN][1000 genomes]
rs11685932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11894529	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs13005285	0.80[CEU][hapmap];0.91[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1596016	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1816753	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2119504	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2241876	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs2241877	0.87[CHB][hapmap];0.84[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs2289475	0.80[CEU][hapmap];0.95[CHB][hapmap];0.92[ASN][1000 genomes]
rs35812841	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3749079	0.86[ASN][1000 genomes]
rs3792110	0.80[CEU][hapmap];0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs4663136	0.84[CEU][hapmap];0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs6431259	0.87[ASN][1000 genomes]
rs6431262	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[ASN][1000 genomes]
rs6431270	0.82[ASN][1000 genomes]
rs6431655	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6737398	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6754677	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6861	0.80[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[ASN][1000 genomes]
rs7563345	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7587633	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs930449	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6431659	ECEL1P2	cis	parietal	SCAN
rs6431659	ATG16L1	cis	cerebellum	SCAN
rs6431659	SCARNA5	cis	parietal	SCAN
rs6431659	SCARNA5	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234161400-234170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:234161400-234170600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:234161400-234170800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:234161600-234167600	Weak transcription	Stomach Mucosa	stomach
5	chr2:234161800-234169000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:234161800-234171800	Weak transcription	Fetal Kidney	kidney
7	chr2:234161800-234180600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:234162200-234205200	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:234162200-234205200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr2:234162400-234170000	Weak transcription	Fetal Brain Male	brain
11	chr2:234162400-234192000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
12	chr2:234162400-234196400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:234162400-234205200	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr2:234162400-234205400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:234162600-234176200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:234162600-234188600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr2:234162600-234192400	Strong transcription	Osteobl	bone
18	chr2:234162600-234205000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:234162600-234205200	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:234162800-234167800	Weak transcription	Brain Hippocampus Middle	brain
21	chr2:234162800-234170200	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr2:234162800-234194000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:234162800-234197000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr2:234162800-234205600	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:234163000-234167400	Weak transcription	Brain Substantia Nigra	brain
26	chr2:234163000-234170200	Strong transcription	Primary B cells from peripheral blood	blood
27	chr2:234163000-234170800	Weak transcription	Fetal Heart	heart
28	chr2:234163000-234175600	Strong transcription	Fetal Thymus	thymus
29	chr2:234163000-234176200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:234163000-234192200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr2:234163000-234192200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr2:234163200-234168000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr2:234163200-234169000	Weak transcription	Pancreas	Pancrea
34	chr2:234163200-234169400	Weak transcription	NHLF	lung
35	chr2:234163200-234175600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:234163200-234177800	Strong transcription	NHEK	skin
37	chr2:234163200-234188000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr2:234163200-234188800	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:234163200-234206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:234163400-234167600	Weak transcription	Psoas Muscle	Psoas
41	chr2:234163800-234188600	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr2:234163800-234189000	Strong transcription	Rectal Mucosa Donor 31	rectum
43	chr2:234164000-234175400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:234164000-234175600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr2:234164000-234177400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr2:234164200-234168200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:234164200-234169000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr2:234164200-234169400	Strong transcription	HSMM	muscle
49	chr2:234164200-234176800	Strong transcription	Fetal Brain Female	brain
50	chr2:234164200-234178800	Strong transcription	Fetal Lung	lung

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