Variant report

Variant	rs6711574
Chromosome Location	chr2:99378801-99378802
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99373723..99375760-chr2:99377966..99380298,2	MCF-7	breast:
2	chr2:99377533..99379343-chr2:99387300..99389873,2	MCF-7	breast:
3	chr2:99352512..99355304-chr2:99377484..99380437,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C2orf55-1	chr2:99378401-99379041	XLOC_002221
2	lnc-C2orf55-1	chr2:99378401-99379041	ENSG00000226791.3

Variant related genes	Relation type
ENSG00000226791	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12464562	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12467276	0.87[MEX][hapmap]
rs12468086	0.87[MEX][hapmap]
rs13012495	0.80[EUR][1000 genomes]
rs17021941	0.81[MEX][hapmap]
rs17755756	1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34091873	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34852807	0.80[EUR][1000 genomes]
rs4539843	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6756691	0.93[EUR][1000 genomes]
rs882164	0.87[MEX][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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6711574	RFX8	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99372200-99380800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr2:99373800-99388000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr2:99374600-99383000	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr2:99374600-99383200	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:99374800-99379000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:99374800-99379000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:99374800-99379000	Weak transcription	Right Atrium	heart
8	chr2:99374800-99379200	Weak transcription	Left Ventricle	heart
9	chr2:99374800-99379400	Weak transcription	Colonic Mucosa	Colon
10	chr2:99374800-99381000	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr2:99374800-99381400	Enhancers	Primary T cells fromperipheralblood	blood
12	chr2:99374800-99382000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:99375000-99379400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:99375200-99379400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr2:99375200-99381000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:99375200-99386200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:99375200-99386400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:99376400-99379600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:99376400-99379800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr2:99376800-99380600	Enhancers	Monocytes-CD14+_RO01746	blood
21	chr2:99376800-99382200	Weak transcription	Duodenum Mucosa	Duodenum
22	chr2:99376800-99384600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr2:99377000-99381600	Enhancers	GM12878-XiMat	blood
24	chr2:99377000-99382200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr2:99377000-99382200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr2:99377000-99385000	Weak transcription	Spleen	Spleen
27	chr2:99377000-99386400	Weak transcription	Esophagus	oesophagus
28	chr2:99377400-99380600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:99377600-99379200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr2:99377600-99379400	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr2:99377600-99379400	Enhancers	Fetal Brain Male	brain
32	chr2:99377600-99379800	Enhancers	HepG2	liver
33	chr2:99377800-99379000	Enhancers	Brain Hippocampus Middle	brain
34	chr2:99377800-99379400	Enhancers	Fetal Brain Female	brain
35	chr2:99377800-99379400	Enhancers	Fetal Muscle Leg	muscle
36	chr2:99377800-99379400	Enhancers	Placenta	Placenta
37	chr2:99377800-99383800	Weak transcription	HUVEC	blood vessel
38	chr2:99378000-99379200	Enhancers	Primary T cells from cord blood	blood
39	chr2:99378000-99379200	Enhancers	Brain Substantia Nigra	brain
40	chr2:99378000-99379800	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr2:99378400-99379200	Enhancers	Brain Cingulate Gyrus	brain
42	chr2:99378400-99379600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr2:99378400-99382600	Weak transcription	Pancreas	Pancrea
44	chr2:99378400-99383200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:99378400-99385000	Weak transcription	Lung	lung
46	chr2:99378400-99385000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:99378400-99389400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr2:99378600-99379400	Genic enhancers	Dnd41	blood
49	chr2:99378600-99382200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:99378600-99382600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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