Variant report

Variant	rs13410179
Chromosome Location	chr2:191319061-191319062
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:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM194B-3	chr2:191318818-191319247	ENSG00000272979.1

Variant related genes	Relation type
ENSG00000151690	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10169169	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10171376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10173975	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10179262	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10185147	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10189140	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10202274	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10204342	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10208737	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10209340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10211375	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10737936	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs11553601	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11695439	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[ASN][1000 genomes]
rs13031452	0.94[ASN][1000 genomes]
rs13384743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13386210	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13388162	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13395233	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13398741	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs13405215	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13412663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13412823	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13412835	0.92[ASN][1000 genomes]
rs13412879	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13417310	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13418943	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13429315	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1837686	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2354877	0.94[GIH][hapmap]
rs3811608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4283453	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4853712	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs56715527	0.90[ASN][1000 genomes]
rs58210597	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58253207	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58433478	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58708643	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6434401	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs6717050	0.91[ASN][1000 genomes]
rs72903349	0.89[ASN][1000 genomes]
rs72903383	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72905242	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73054092	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7556716	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7560045	0.94[ASN][1000 genomes]
rs7562013	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7564107	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7574844	0.94[ASN][1000 genomes]
rs7584379	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7594994	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7609330	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs894072	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[ASN][1000 genomes]
rs8962	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9288174	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.94[ASN][1000 genomes]
rs9967829	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33134	chr2:191318791-191365710	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv962094	chr2:191318806-191324621	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13410179	MFSD6	cis	parietal	SCAN
rs13410179	ASNSD1	cis	parietal	SCAN
rs13410179	FLJ20160	cis	multi-tissue	Pritchard
rs13410179	TMEM194B	cis	cerebellum	SCAN
rs13410179	MFSD6	cis	lymphoblastoid	seeQTL
rs13410179	FLJ20160	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:191308800-191320000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr2:191308800-191327200	Weak transcription	Right Atrium	heart
19	chr2:191309200-191322400	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:191309400-191331400	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:191310200-191323600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:191310400-191331600	Weak transcription	Stomach Mucosa	stomach
23	chr2:191311400-191324200	Weak transcription	Fetal Heart	heart
24	chr2:191311600-191321400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:191311600-191321400	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:191311600-191331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr2:191311800-191324600	Weak transcription	Left Ventricle	heart
28	chr2:191311800-191331400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:191311800-191331400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr2:191311800-191331600	Weak transcription	Ovary	ovary
31	chr2:191312000-191332400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:191312200-191321200	Weak transcription	Fetal Stomach	stomach
33	chr2:191312200-191324400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:191313000-191321200	Weak transcription	Gastric	stomach
35	chr2:191313000-191331400	Weak transcription	HSMMtube	muscle
36	chr2:191313000-191333600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:191313800-191323600	Weak transcription	Brain Anterior Caudate	brain
38	chr2:191314000-191331600	Weak transcription	Fetal Kidney	kidney
39	chr2:191315800-191327400	Weak transcription	Spleen	Spleen
40	chr2:191316200-191319200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr2:191316400-191321400	Weak transcription	Lung	lung
42	chr2:191316600-191321800	Weak transcription	Primary B cells from cord blood	blood
43	chr2:191316600-191323400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr2:191316600-191324600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr2:191316600-191325200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:191316600-191331200	Weak transcription	NHLF	lung
47	chr2:191317000-191323600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr2:191317200-191319400	Strong transcription	Primary T cells from cord blood	blood
49	chr2:191317400-191319400	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:191317400-191319400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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