Variant report

Variant	rs6431655
Chromosome Location	chr2:234162415-234162416
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:234161754..234164546-chr2:234176635..234178201,2	K562	blood:
2	chr2:234160919..234163001-chr2:234739570..234741620,2	MCF-7	breast:
3	chr2:234161693..234166047-chr2:234167019..234170688,4	MCF-7	breast:
4	chr2:234161380..234162946-chr2:234262320..234263991,2	MCF-7	breast:
5	chr2:234161285..234164496-chr2:234179412..234182858,4	MCF-7	breast:
6	chr2:234161323..234164097-chr2:234164693..234167813,4	K562	blood:

Variant related genes	Relation type
ENSG00000077044	Chromatin interaction
ENSG00000243637	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1045095	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10929033	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11685932	0.87[CHB][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11894529	0.80[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13005285	0.95[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs1816753	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2119504	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2241876	0.84[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2241877	0.85[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289475	0.89[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35812841	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3792110	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4663136	0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs4663429	0.92[ASN][1000 genomes]
rs6431259	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6431262	0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap]
rs6431270	0.89[ASN][1000 genomes]
rs6431659	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]
rs6705993	0.82[ASN][1000 genomes]
rs6717493	0.81[ASN][1000 genomes]
rs6717560	0.86[EUR][1000 genomes]
rs6737398	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6754677	0.87[CHB][hapmap]
rs6861	0.80[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7574945	0.80[ASN][1000 genomes]
rs7587051	0.82[CHB][hapmap]
rs7587633	0.89[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7595748	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6431655	SCARNA5	cis	parietal	SCAN
rs6431655	ATG16L1	cis	cerebellum	SCAN
rs6431655	GIGYF2	cis	cerebellum	SCAN
rs6431655	RFT1	trans	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234160000-234163800	Active TSS	GM12878-XiMat	blood
2	chr2:234161000-234163000	Enhancers	Fetal Heart	heart
3	chr2:234161200-234163200	Enhancers	Spleen	Spleen
4	chr2:234161400-234162600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr2:234161400-234162800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:234161400-234163000	Enhancers	Gastric	stomach
7	chr2:234161400-234164400	Weak transcription	Placenta	Placenta
8	chr2:234161400-234165200	Weak transcription	Ovary	ovary
9	chr2:234161400-234166800	Weak transcription	Esophagus	oesophagus
10	chr2:234161400-234170600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:234161400-234170600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:234161400-234170800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr2:234161600-234162600	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
14	chr2:234161600-234162600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr2:234161600-234162600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr2:234161600-234162600	Enhancers	Adipose Nuclei	Adipose
17	chr2:234161600-234162600	Weak transcription	Aorta	Aorta
18	chr2:234161600-234162800	Enhancers	Rectal Smooth Muscle	rectum
19	chr2:234161600-234162800	Enhancers	Right Ventricle	heart
20	chr2:234161600-234163000	Enhancers	Brain Substantia Nigra	brain
21	chr2:234161600-234163200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr2:234161600-234163200	Transcr. at gene 5' and 3'	Dnd41	blood
23	chr2:234161600-234163400	Transcr. at gene 5' and 3'	A549	lung
24	chr2:234161600-234165000	Enhancers	Colon Smooth Muscle	Colon
25	chr2:234161600-234167600	Weak transcription	Stomach Mucosa	stomach
26	chr2:234161800-234162600	Enhancers	Primary B cells from cord blood	blood
27	chr2:234161800-234162600	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:234161800-234162600	Flanking Active TSS	HepG2	liver
29	chr2:234161800-234162800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr2:234161800-234162800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:234161800-234162800	Enhancers	Brain Cingulate Gyrus	brain
32	chr2:234161800-234162800	Enhancers	Fetal Intestine Small	intestine
33	chr2:234161800-234162800	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr2:234161800-234162800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:234161800-234162800	Weak transcription	Psoas Muscle	Psoas
36	chr2:234161800-234163000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr2:234161800-234163200	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr2:234161800-234163200	Enhancers	Liver	Liver
39	chr2:234161800-234163200	Enhancers	Brain Angular Gyrus	brain
40	chr2:234161800-234163200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr2:234161800-234164000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr2:234161800-234164200	Genic enhancers	Primary T cells fromperipheralblood	blood
43	chr2:234161800-234164200	Enhancers	HUVEC	blood vessel
44	chr2:234161800-234164400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:234161800-234164600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:234161800-234164600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr2:234161800-234166000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr2:234161800-234166200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr2:234161800-234169000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr2:234161800-234171800	Weak transcription	Fetal Kidney	kidney

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