Variant report

Variant	rs2851104
Chromosome Location	chr11:74853813-74853814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CBX3	chr11:74853804-74854735	HCT-116	colon:	n/a	n/a
2	CTCF	chr11:74853720-74853870	BE2_C	brain:	n/a	n/a
3	MAX	chr11:74853813-74854731	A549	lung:	n/a	chr11:74854274-74854290 chr11:74854272-74854282 chr11:74854271-74854281 chr11:74854271-74854282 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854271-74854282 chr11:74854268-74854283 chr11:74854600-74854616 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854271-74854282 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854273-74854282 chr11:74854271-74854281 chr11:74854267-74854286 chr11:74854387-74854396 chr11:74854271-74854282
4	MXI1	chr11:74853280-74854712	IMR90	lung:	n/a	chr11:74854273-74854282
5	MAX	chr11:74853678-74854847	HCT-116	colon:	n/a	chr11:74854274-74854290 chr11:74854272-74854282 chr11:74854271-74854281 chr11:74854271-74854282 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854271-74854282 chr11:74854268-74854283 chr11:74854600-74854616 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854271-74854282 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854273-74854282 chr11:74854271-74854281 chr11:74854267-74854286 chr11:74854387-74854396 chr11:74854271-74854282
6	CTCF	chr11:74853740-74853890	GM12864	blood:	n/a	n/a
7	JUN	chr11:74853451-74854863	K562	blood:	n/a	chr11:74854175-74854184 chr11:74854387-74854396 chr11:74854386-74854395
8	MAX	chr11:74853763-74854716	K562	blood:	n/a	chr11:74854274-74854290 chr11:74854272-74854282 chr11:74854271-74854281 chr11:74854271-74854282 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854271-74854282 chr11:74854268-74854283 chr11:74854600-74854616 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854271-74854282 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854273-74854282 chr11:74854271-74854281 chr11:74854267-74854286 chr11:74854387-74854396 chr11:74854271-74854282
9	CTCF	chr11:74853720-74853870	MCF-7	breast:	n/a	n/a
10	CTCF	chr11:74853700-74853850	GM12875	blood:	n/a	n/a
11	MAX	chr11:74853740-74854797	A549	lung:	n/a	chr11:74854274-74854290 chr11:74854272-74854282 chr11:74854271-74854281 chr11:74854271-74854282 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854271-74854282 chr11:74854268-74854283 chr11:74854600-74854616 chr11:74854270-74854283 chr11:74854272-74854281 chr11:74854271-74854282 chr11:74854272-74854281 chr11:74854272-74854282 chr11:74854273-74854282 chr11:74854271-74854281 chr11:74854267-74854286 chr11:74854387-74854396 chr11:74854271-74854282

No.	Distal block	Cell Line	Cell type
1	chr11:74851665..74854336-chr11:74855499..74858438,2	MCF-7	breast:
2	chr11:74849283..74850784-chr11:74852080..74854069,2	K562	blood:
3	chr11:74853112..74855934-chr11:74951491..74955339,4	K562	blood:
4	chr11:74853654..74855652-chr11:74858777..74860606,2	K562	blood:

Variant related genes	Relation type
ENSG00000255395	TF binding region
ENSG00000255136	Chromatin interaction
ENSG00000261594	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10899075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1676878	0.87[AFR][1000 genomes]
rs1944615	0.85[ASN][1000 genomes]
rs1944616	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2018251	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2156656	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2465290	0.91[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.90[MKK][hapmap];0.88[ASN][1000 genomes]
rs2712786	0.85[JPT][hapmap]
rs2712788	0.82[CHB][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap]
rs2712793	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712794	0.80[ASN][1000 genomes]
rs2712795	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712797	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712799	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712800	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2712801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712802	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2712806	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2712808	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712809	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712811	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2712814	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2712815	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2712816	0.91[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.92[JPT][hapmap];0.90[MKK][hapmap];0.88[ASN][1000 genomes]
rs2712817	0.88[ASN][1000 genomes]
rs2712818	0.82[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap]
rs2851065	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851067	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851068	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851069	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2851070	0.89[AFR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851071	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851072	1.00[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2851075	0.90[ASW][hapmap];0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.90[MKK][hapmap];0.88[ASN][1000 genomes]
rs2851078	0.82[CHB][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap]
rs2851079	0.92[JPT][hapmap]
rs2851080	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2851081	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2851082	0.85[JPT][hapmap]
rs2851084	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs2851086	0.85[JPT][hapmap]
rs2851093	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2851095	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851097	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2851103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2851105	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2851107	0.81[ASN][1000 genomes]
rs2851109	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2851112	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4335576	0.85[JPT][hapmap]
rs4435030	0.91[ASW][hapmap];0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs4944067	0.85[JPT][hapmap]
rs7117575	0.82[ASW][hapmap];0.82[LWK][hapmap];0.90[MKK][hapmap];0.85[YRI][hapmap]
rs7121374	0.85[JPT][hapmap]
rs870505	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs870506	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs875482	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2851104	RNF169	cis	cerebellum	SCAN
rs2851104	FCHSD2	cis	cerebellum	SCAN
rs2851104	CRYGD	trans	parietal	SCAN
rs2851104	THRSP	cis	parietal	SCAN
rs2851104	INPPL1	cis	parietal	SCAN
rs2851104	FBXO42	trans	parietal	SCAN
rs2851104	XRRA1	cis	cerebellum	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74851400-74855600	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr11:74851600-74855800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr11:74851800-74854400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr11:74852000-74854000	Weak transcription	Fetal Intestine Large	intestine
5	chr11:74852000-74854000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:74852000-74854400	Weak transcription	Liver	Liver
7	chr11:74852000-74861600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr11:74852200-74855200	Weak transcription	Fetal Intestine Small	intestine
9	chr11:74852400-74856000	Enhancers	K562	blood
10	chr11:74852400-74858200	Weak transcription	Esophagus	oesophagus
11	chr11:74852400-74861000	Weak transcription	Stomach Mucosa	stomach
12	chr11:74853000-74854200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr11:74853000-74854400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr11:74853000-74854400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr11:74853000-74855600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr11:74853200-74855600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr11:74853200-74855800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr11:74853400-74854400	Enhancers	Primary T cells from cord blood	blood
19	chr11:74853400-74855600	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr11:74853600-74854000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr11:74853600-74854200	Enhancers	A549	lung
22	chr11:74853600-74854400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:74853600-74854400	Enhancers	Dnd41	blood
24	chr11:74853600-74854800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr11:74853600-74854800	Enhancers	Hela-S3	cervix
26	chr11:74853600-74855400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr11:74853600-74855400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:74853600-74855800	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr11:74853600-74855800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr11:74853600-74855800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr11:74853600-74855800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:74853600-74855800	Enhancers	Fetal Muscle Leg	muscle
33	chr11:74853800-74854000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr11:74853800-74854200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr11:74853800-74854200	Enhancers	Brain Cingulate Gyrus	brain
36	chr11:74853800-74854400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr11:74853800-74854400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr11:74853800-74854400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:74853800-74854400	Enhancers	Right Atrium	heart
40	chr11:74853800-74854400	Enhancers	Stomach Smooth Muscle	stomach
41	chr11:74853800-74854600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:74853800-74854600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr11:74853800-74854600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr11:74853800-74854600	Enhancers	NHDF-Ad	bronchial
45	chr11:74853800-74854800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr11:74853800-74854800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:74853800-74854800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:74853800-74854800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr11:74853800-74855000	Enhancers	Colonic Mucosa	Colon
50	chr11:74853800-74855400	Enhancers	Primary B cells from peripheral blood	blood

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