Variant report

Variant	rs6441977
Chromosome Location	chr3:46450072-46450073
allele	A/G
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	POLR2A	chr3:46448132-46450759	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:46447015..46450131-chr3:46450692..46453311,4	K562	blood:

Variant related genes	Relation type
ENSG00000223552	TF binding region
CCRL2	TF binding region
ENSG00000121797	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11574428	1.00[CEU][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap]
rs2157062	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs6762266	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs6791599	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap]
rs916093	1.00[CEU][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv3323840	chr3:46352348-46497196	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv3389382	chr3:46352798-46496696	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6441977	LTF	cis	parietal	SCAN
rs6441977	ZNF501	cis	cerebellum	SCAN
rs6441977	ABHD5	cis	cerebellum	SCAN
rs6441977	ALS2CL	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46438800-46459800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:46446200-46450200	Enhancers	Fetal Lung	lung
3	chr3:46446800-46450600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:46448200-46450200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr3:46448200-46452000	Enhancers	Dnd41	blood
6	chr3:46448400-46450200	Flanking Active TSS	HSMM	muscle
7	chr3:46448400-46450200	Flanking Active TSS	Osteobl	bone
8	chr3:46448400-46450400	Enhancers	Fetal Heart	heart
9	chr3:46448600-46450200	Flanking Active TSS	HUVEC	blood vessel
10	chr3:46448600-46460000	Weak transcription	Gastric	stomach
11	chr3:46448800-46450400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:46449200-46450400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:46449200-46451400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:46449200-46451800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:46449400-46450200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr3:46449400-46450200	Enhancers	Fetal Stomach	stomach
17	chr3:46449400-46450200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr3:46449400-46450200	Enhancers	NHLF	lung
19	chr3:46449400-46450400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr3:46449400-46450400	Enhancers	Fetal Muscle Leg	muscle
21	chr3:46449400-46450600	Enhancers	Left Ventricle	heart
22	chr3:46449400-46450600	Enhancers	NH-A	brain
23	chr3:46449400-46450800	Enhancers	Psoas Muscle	Psoas
24	chr3:46449400-46453000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:46449600-46450200	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr3:46449600-46450200	Enhancers	Fetal Intestine Large	intestine
27	chr3:46449600-46450200	Enhancers	Right Atrium	heart
28	chr3:46449600-46450200	Enhancers	Right Ventricle	heart
29	chr3:46449600-46450200	Enhancers	HSMMtube	muscle
30	chr3:46449600-46450400	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr3:46449600-46450800	Genic enhancers	Primary T cells from cord blood	blood
32	chr3:46449600-46451000	Genic enhancers	Fetal Intestine Small	intestine
33	chr3:46449600-46451200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:46449600-46451200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr3:46449600-46452000	Enhancers	K562	blood
36	chr3:46449600-46453800	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:46449600-46454000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:46449600-46457600	Weak transcription	Primary B cells from cord blood	blood
39	chr3:46449800-46450200	Enhancers	Placenta	Placenta
40	chr3:46449800-46450200	Enhancers	NHDF-Ad	bronchial
41	chr3:46449800-46450400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:46449800-46450400	Genic enhancers	Thymus	Thymus
43	chr3:46449800-46451000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:46449800-46451000	Genic enhancers	Fetal Thymus	thymus
45	chr3:46449800-46451200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr3:46449800-46451400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:46449800-46451800	Enhancers	Primary hematopoietic stem cells	blood
48	chr3:46449800-46452000	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr3:46449800-46453800	Weak transcription	Small Intestine	intestine
50	chr3:46450000-46450200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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