Variant report

Variant	rs13409841
Chromosome Location	chr2:191318776-191318777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:191318515..191323057-chr2:191332501..191335066,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10182754	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10193212	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10931452	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12475614	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12613807	0.81[CEU][hapmap];0.86[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693574	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693575	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12998288	0.85[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs13020324	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354878	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35095338	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3811607	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4340549	0.83[LWK][hapmap]
rs4853507	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4853702	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4853705	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4853710	0.84[LWK][hapmap]
rs4853711	0.81[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4853713	0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6434391	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6707691	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7557681	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7564829	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7596573	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7603607	0.85[CHB][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9646748	0.96[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9646815	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13409841	C2orf88	cis	parietal	SCAN
rs13409841	HIBCH	cis	cerebellum	SCAN
rs13409841	ZC3H15	cis	cerebellum	SCAN
rs13409841	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL
rs13409841	MFSD6	cis	Artery Tibial	GTEx
rs13409841	TMEM194B	cis	Adipose Subcutaneous	GTEx
rs13409841	MFSD6	cis	parietal	SCAN
rs13409841	FLJ20160	cis	multi-tissue	Pritchard
rs13409841	MFSD6	cis	lymphoblastoid	seeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:191302200-191319200	Weak transcription	Fetal Intestine Small	intestine
2	chr2:191302200-191321200	Weak transcription	Esophagus	oesophagus
3	chr2:191302400-191331000	Weak transcription	A549	lung
4	chr2:191302800-191319400	Weak transcription	Fetal Brain Female	brain
5	chr2:191302800-191320200	Weak transcription	Fetal Thymus	thymus
6	chr2:191302800-191321200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:191303400-191321000	Weak transcription	Thymus	Thymus
8	chr2:191303400-191321200	Weak transcription	Dnd41	blood
9	chr2:191303600-191321000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr2:191303800-191321000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:191303800-191331600	Weak transcription	Brain Germinal Matrix	brain
12	chr2:191303800-191332600	Weak transcription	Fetal Intestine Large	intestine
13	chr2:191306600-191321000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:191306600-191351000	Weak transcription	Pancreas	Pancrea
15	chr2:191307600-191322600	Weak transcription	Aorta	Aorta
16	chr2:191308000-191328800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:191308800-191319000	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:191308800-191320000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:191308800-191327200	Weak transcription	Right Atrium	heart
20	chr2:191309200-191322400	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:191309400-191331400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:191310200-191323600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr2:191310400-191331600	Weak transcription	Stomach Mucosa	stomach
24	chr2:191311400-191324200	Weak transcription	Fetal Heart	heart
25	chr2:191311600-191321400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:191311600-191321400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr2:191311600-191331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:191311800-191324600	Weak transcription	Left Ventricle	heart
29	chr2:191311800-191331400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr2:191311800-191331400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:191311800-191331600	Weak transcription	Ovary	ovary
32	chr2:191312000-191332400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr2:191312200-191321200	Weak transcription	Fetal Stomach	stomach
34	chr2:191312200-191324400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr2:191313000-191321200	Weak transcription	Gastric	stomach
36	chr2:191313000-191331400	Weak transcription	HSMMtube	muscle
37	chr2:191313000-191333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr2:191313800-191323600	Weak transcription	Brain Anterior Caudate	brain
39	chr2:191314000-191331600	Weak transcription	Fetal Kidney	kidney
40	chr2:191315800-191327400	Weak transcription	Spleen	Spleen
41	chr2:191316200-191318800	Enhancers	Brain Hippocampus Middle	brain
42	chr2:191316200-191319200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr2:191316400-191321400	Weak transcription	Lung	lung
44	chr2:191316600-191321800	Weak transcription	Primary B cells from cord blood	blood
45	chr2:191316600-191323400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr2:191316600-191324600	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:191316600-191325200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr2:191316600-191331200	Weak transcription	NHLF	lung
49	chr2:191317000-191323600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr2:191317200-191319400	Strong transcription	Primary T cells from cord blood	blood

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