Variant report

Variant	rs6844681
Chromosome Location	chr4:143247240-143247241
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:143246175..143247898-chr4:143247988..143249905,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs2627802	0.93[GIH][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs2627814	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635427	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635428	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2636671	0.92[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.88[EUR][1000 genomes]
rs2646088	0.82[EUR][1000 genomes]
rs2646095	0.83[ASW][hapmap]
rs2646096	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs960679	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6844681	NDUFC1	cis	parietal	SCAN
rs6844681	C4orf49	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143217600-143260800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:143233800-143257200	Weak transcription	Left Ventricle	heart
3	chr4:143234800-143271800	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:143235600-143266400	Weak transcription	NHEK	skin
5	chr4:143236000-143252000	Weak transcription	HSMM	muscle
6	chr4:143236200-143257000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr4:143236200-143257200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:143236200-143257600	Weak transcription	HMEC	breast
9	chr4:143236400-143247400	Weak transcription	Fetal Intestine Small	intestine
10	chr4:143237200-143251200	Weak transcription	Stomach Mucosa	stomach
11	chr4:143237400-143252000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr4:143237600-143251000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr4:143240400-143257000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:143244400-143253800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr4:143244400-143256800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:143244600-143256800	Weak transcription	Dnd41	blood
17	chr4:143245200-143247600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr4:143245400-143247400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:143245400-143248000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr4:143245600-143249600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr4:143245600-143253000	Enhancers	Primary T helper cells fromperipheralblood	blood
22	chr4:143245600-143253600	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr4:143245600-143257600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:143245800-143247400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:143245800-143257200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:143246000-143257000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr4:143246200-143249200	Weak transcription	Psoas Muscle	Psoas
28	chr4:143246400-143247800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr4:143246400-143252200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr4:143246600-143248000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr4:143246600-143267800	Weak transcription	Primary T cells from cord blood	blood
32	chr4:143246800-143249200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:143246800-143251200	Weak transcription	Fetal Heart	heart
34	chr4:143246800-143251400	Weak transcription	HSMMtube	muscle
35	chr4:143246800-143257200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr4:143247200-143247400	Enhancers	Small Intestine	intestine

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